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LinuxForHealth FHIR Server User's Guide

1 Overview

The LinuxForHealth FHIR Server implements the HL7 FHIR HTTP API and supports the full set of FHIR-defined resource types. This FHIR server is intended to be a common component for providing FHIR capabilities within health services and solutions.

2 Installation

2.1 Installing a new server

  1. Prereqs: The LinuxForHealth FHIR Server requires Java 11 and has been tested with OpenJDK 11. To install Java on your system, we recommend downloading and installing OpenJDK 11 from https://adoptium.net/.

  2. To install the LinuxForHealth FHIR Server, build or download the fhir-install zip installer. The Maven build creates the zip package under fhir-install/target. Alternatively, releases are available from the Releases tab.

  3. Unzip the .zip package into a clean directory (referred to as fhir-installer here):

    mkdir fhir-installer
    cd fhir-installer
    unzip fhir-server-distribution.zip
  4. Determine an install location for the OpenLiberty server and the LinuxForHealth FHIR Server webapp. Example: /opt/ibm/fhir-server

  5. Run the install.sh/.bat script to install the server:

    ./fhir-server-dist/install.sh /opt/ibm/fhir-server

    This step installs the OpenLiberty runtime and the LinuxForHealth FHIR Server web application. The Liberty runtime is installed in a directory called wlp within the installation directory that you specify. For example, in the preceding command, the root directory of the Liberty server runtime would be /opt/ibm/fhir-server/wlp.

  6. Configure the fhir-server’s server.xml file as needed by completing the following steps:

    • Configure the ports that the server listen on. The server is installed with only port 9443 (HTTPS) enabled by default. To change the port numbers, modify the values in the httpEndpoint element.
    • Configure a server keystore and truststore. The LinuxForHealth FHIR Server is installed with a default keystore file that contains a single self-signed certificate for localhost. For production use, you must create and configure your own keystore and truststore files for the FHIR server deployment (that is, generate your own server certificate or obtain a trusted certificate, and then share the public key certificate with API consumers so that they can insert it into their client-side truststore). The keystore and truststore files are used along with the server’s HTTPS endpoint and the FHIR server’s client-certificate-based authentication protocol to secure the FHIR server’s endpoint. For more information, see Section 5.2 Keystores, truststores, and the FHIR server.
    • Configure an appropriate user registry. The FHIR server is installed with a basic user registry that contains a single user named fhiruser. For production use, it’s best to configure your own user registry. For more information about configuring user registries, see the OpenLiberty documentation.

    To override the default fhiruser’s password, one may set an Environment variable FHIR_USER_PASSWORD and for the fhiradmin’s password one may set an Environment variable FHIR_ADMIN_PASSWORD.

  7. Make sure that your selected database product is running and ready to accept requests as needed:

    • By default, the FHIR server is installed with the JDBC persistence layer configured to use an Embedded Derby database. When using the ibmcom/ibm-fhir-server docker image, set the BOOTSTRAP_DB environment variable to true in order to bootstrap this database. For any other configuration, note the database host and port and, if necessary, create a user with privileges for deploying the schema.
  8. Create and deploy the LinuxForHealth FHIR Server database schema as needed:

    • By default, the FHIR server is installed with the JDBC persistence layer configured to use an Embedded Derby database. When using the ibmcom/ibm-fhir-server docker image, set the BOOTSTRAP_DB environment variable to true in order to bootstrap this database. For any other configuration, use the fhir-persistence-schema module to create and deploy the database schema.
  9. Configure the fhir-server-config.json1 configuration file as needed:

  10. To start and stop the server, use the Liberty server command:

<WLP_HOME>/bin/server start fhir-server
<WLP_HOME>/bin/server stop fhir-server
  1. After you start the server, you can verify that it’s running properly by invoking the $healthcheck endpoint like this:
curl -k -u '<username>:<password>' 'https://<host>:<port>/fhir-server/api/v4/$healthcheck'

where <username> is one of the users configured in server.xml (default is fhiruser).
Use single quotes around the URL to prevent $healthcheck from being evaluated as an environment variable on unix-based operating systems.

One should see an empty body in the response with a HTTP Response Code 200.

For more information about the capabilities of the implementation, see Conformance.

2.2 Upgrading an existing server

The LinuxForHealth FHIR Server does not include an upgrade installer. To upgrade a server to the next version, install the new version to a separate location and copy the configuration files from your existing installation (reconciling any configuration-related changes from the new release in the process).

To manage database updates over time, the LinuxForHealth FHIR Server uses custom tools from the fhir-database-utils project. Through the use of a metadata table, the database utilities can detect the currently installed version of the database schema and apply any new changes that are needed to bring the database to the current level.

Complete the following steps to upgrade the server:

  1. Run the fhir-installer on a separate server.
  2. Configure the new server as appropriate (fhir-server/server.xml and anything under the fhir-server/configDropins, fhir-server/config, and fhir-server/userlib directories).
  3. Back up your database.
  4. Run the migration program (see Section 3.3.1.1 Supported databases).
  5. Disable traffic to the old server and enable traffic to the new server.

2.3 Docker

The LinuxForHealth FHIR Server includes a Docker image ibmcom/ibm-fhir-server.

Note, logging for the LinuxForHealth FHIR Server docker image is to stderr and stdout, and is picked up by Logging agents.

The LinuxForHealth FHIR Server is configured using Environment variables using:

Environment VariableDescription
DISABLED_OPERATIONSA comma-separated list of operations which are disabled on the LinuxForHealth FHIR Server, for example, validate,import. Note, do not include the dollar sign $

Development-Only: If you are using the LinuxForHealth FHIR Server on a development machine with under 3.25G of RAM. You should download jvm-dev.options and mount it when starting the Docker container. You can use the following pattern for starting up in a restricted test environment (or build your own layer).

docker run -d -p 9443:9443 -e BOOTSTRAP_DB=true \
-v $(pwd)/jvm-dev.options:/config/configDropins/default/jvm.options \
ibmcom/ibm-fhir-server

3 Configuration

This chapter contains information about the various ways in which the LinuxForHealth FHIR Server can be configured by users.

3.1 Liberty server configuration

The LinuxForHealth FHIR Server is built on the open source OpenLiberty project but also works on the commercial IBM WebSphere Liberty. In documentation and elsewhere, we use Liberty to refer to either/or.

As a Liberty application, the LinuxForHealth FHIR Server is configurable like any other Liberty server. See https://openliberty.io/docs/latest/reference/config/server-configuration-overview.html for more information.

By default, we include:

  • server.xml with core server details like the Liberty features, HTTP properties, application info, and a default user registry
  • jvm.options with TLS and heap size settings
  • server.env with timezone set to UTC
  • configDropins with server.xml dropins sorted into disabled, defaults, and overrides

3.1.1 Encoded passwords

In the examples within the following sections, you’ll see the default password change-password. In order to secure your server, these values should be changed.

For example, the basic user registry in the default server.xml defines users fhiruser and fhiradmin and variables FHIR_USER_PASSWORD and FHIR_ADMIN_PASSWORD, each with a default value of change-password.

These variables can be changed by setting environment variables by the same name. Alternatively, users can change the server.xml or use Liberty configDropins to change the values.

Optionally, server.xml values can be encoded via the Liberty securityUtility command. For example, to encode a string value with the default {xor} encoding, run the following command:

<WLP_HOME>/bin/securityUtility encode stringToEncode

The output of this command can then be copied and pasted into your server.xml or fhir-server-config.json file as needed. The fhir-server-config.json does not support the securityUtility’s {aes} encoding at this time, but per the limits to protection through password encryptiona, this encoding does not provide significant additional security beyond exclusive or (XOR) encoding.

3.1.2 Logging and trace

The default server.xml includes variables for configuring the log output:

<variable name="TRACE_SPEC" defaultValue="*=info"/>
<variable name="TRACE_FILE" defaultValue="trace.log"/>
<variable name="TRACE_FORMAT" defaultValue="BASIC"/>

By default, INFO level messages will go to both the console and a log file at wlp/usr/servers/fhir-server/logs/messages.log. For the ibmcom/ibm-fhir-server docker image, the default is changed to go just to the console.

To enable tracing, set the TRACE_SPEC variable (e.g. by setting an environment variable by the same name) to a :-delimited list of component = level pair values. For example, to turn on tracing for the SQL generated by fhir-persistence-jdbc, set the TRACE_SPEC to org.linuxforhealth.fhir.persistence.jdbc.dao.impl.*=fine:org.linuxforhealth.fhir.database.utils.query.QueryUtil=fine.

By default, that trace output appears alongside the messages.log file in a file named trace.log, but the trace output can be sent to the console instead by setting the TRACE_FILE variable to stdout.

For more information on logging and tracing in Liberty, see https://openliberty.io/docs/latest/log-trace-configuration.html.

3.2 FHIR server configuration

3.2.1 Property names

Configuration properties stored within a fhir-server-config.json file are structured in a hierarchical manner. Here is an example:

{
"fhirServer":{
"core":{
"defaultPrettyPrint":false
}
}
}

Throughout this document, we use a path notation to refer to property names. For example, the name of the defaultPrettyPrint property in the preceding example would be fhirServer/core/defaultPrettyPrint.

3.2.2 Tenant-specific configuration properties

The LinuxForHealth FHIR Server supports certain multi-tenant features. One such feature is the ability to set certain configuration properties on a per-tenant basis.

In general, the configuration properties for a particular tenant are stored in the <WLP_HOME>/usr/servers/fhir-server/config/<tenant-id>/fhir-server-config.json file, where <tenant-id> refers to the tenant’s “short name” or tenant id.

The global configuration is considered to be associated with a tenant named default, so those properties are stored in the <WLP_HOME>/usr/servers/fhir-server/config/default/fhir-server-config.json file.

Similarly, tenant-specific search parameters are found at <WLP_HOME>/usr/servers/fhir-server/config/<tenant-id>/extension-search-parameters.json, whereas the global/default extension search parameters are at <WLP_HOME>/usr/servers/fhir-server/config/default/extension-search-parameters.json.

Search parameters are handled like a single configuration properly; providing a tenant-specific file will override the global/default extension search parameters as defined at FHIRSearchConfiguration.

More information about multi-tenant support can be found in Section 4.9 Multi-tenancy.

3.3 Persistence layer configuration

The LinuxForHealth FHIR Server allows deployers to select a persistence layer implementation that fits their needs. Currently, the server includes a JDBC persistence layer which supports Apache Derby and PostgreSQL. However, Apache Derby is not recommended for production usage.

Before you can configure the server to use the JDBC persistence layer implementation, you first need to prepare the database. This step depends on the database product in use and is covered in more detail in Section 3.3.1.1 Supported databases.

The LinuxForHealth FHIR Server is delivered with a default configuration that is already configured to use the JDBC persistence layer implementation with an Embedded Derby database. This provides the easiest out-of-the-box experience since it requires very little setup.

The LinuxForHealth FHIR Server persistence configuration is split between fhir-server-config.json and the Liberty server.xml and configDropins.

Within fhir-server-config.json, the value of the fhirServer/persistence/factoryClassname is used to instantiate a FHIRPersistence object. By default, the server is configured to use the FHIRPersistenceJDBCFactory:

{
"fhirServer": {
"persistence": {
"factoryClassname": "org.linuxforhealth.fhir.persistence.jdbc.FHIRPersistenceJDBCFactory",
}
}

3.3.1 The JDBC persistence layer

When the FHIRPersistenceJDBCFactory is in use, the fhirServer/persistence/datasources property must specify a mapping from datastore-id values to Liberty datasource definitions. For example, here is the configuration for a datastore with id default that is configured for the jdbc/fhir_default_default datasource of type postgresql:

{
"fhirServer":{
"persistence":{
"factoryClassname":"org.linuxforhealth.fhir.persistence.jdbc.FHIRPersistenceJDBCFactory",
"datasources": {
"default": {
"type": "postgresql",
"currentSchema": "fhirdata",
"jndiName": "jdbc/fhir_default_default"

Both the type and the currentSchema properties are required. The type value must be set to one of the supported JDBC types (currently postgresql, or derby) and it must match the actual database type referenced by the datasource definition. If the type does not match, the behavior is undefined. Because the LinuxForHealth FHIR Server does not quote the schema name in our generated queries, the currentSchema property is effectively case-insensitive.

The jndiName property is optional; it will default to jdbc/fhir_<tenantId>_<dsId> where <tenantId> and <dsId> represent the tenant and datastore ids respectively4.

The datasource definitions themselves are configured in accordance with the Liberty documentation on Relational database connections with JDBC. Previous versions of the LinuxForHealth FHIR Server supported a proxy datasource that allowed for datasource definitions in the fhir-server-config.json, but now Liberty JDBC datasource configuration is used due to benefits related to configuring pool sizes, transaction recovery, and monitoring.

For example, the fhir-server-config snippet from above would have a corresponding Liberty config like this:

<server>
<!-- ============================================================== -->
<!-- TENANT: default; DSID: default; TYPE: read-write -->
<!-- ============================================================== -->
<dataSource id="fhirDefaultDefault" jndiName="jdbc/fhir_default_default" type="javax.sql.XADataSource" statementCacheSize="200" syncQueryTimeoutWithTransactionTimeout="true" validationTimeout="30s">
<jdbcDriver javax.sql.XADataSource="org.postgresql.xa.PGXADataSource" libraryRef="sharedLibPostgres"/>
<properties.postgresql
serverName="postgres"
portNumber="5432"

Datasource elements should not be defined in the main server.xml file but instead should be defined in the configDropins/overrides directory. See the Liberty Profile Server configuration guide for more details and general guidance on creating modular configurations.

The LinuxForHealth FHIR Server is packaged with the following sample datasource definitions at configDropins/disabled:

  • datasource-postgresql.xml
  • datasource-derby.xml

There are 2 libraries defined in the main server.xml that reference the required client drivers for each database type:

  • sharedLibDerby
  • sharedLibPostgres

When a datasource definition is included in a configDropin under configDropins/overrides, this file is picked up when the server starts as indicated by the following AUDIT message:

[AUDIT ] CWWKG0093A: Processing configuration drop-ins resource: <WLP_HOME>/usr/servers/fhir-server/configDropins/overrides/datasource.xml

The LinuxForHealth FHIR Server will look up the tenant and datastore id for each request and use the corresponding JNDI name to obtain a connection for the corresponding datasource.

3.3.1.1 Supported databases

Embedded Derby (default)

If you are using the ibmcom/ibm-fhir-server docker image, you can ask the entrypoint script to create (bootstrap) the database and the schema during startup by setting the BOOTSTRAP_DB environment variable to true.

This database bootstrap step is only supported for Embedded Derby and will only bootstrap the default datastore of the default tenant (the default for requests with no tenant or datastore headers).

Reminder: the Embedded Derby support is designed to support simple getting started scenarios and is not recommended for production use.

<server>
<!-- ============================================================== -->
<!-- This datasource aligns with the Apache Derby database that is -->
<!-- created by the LinuxForHealth FHIR Server's DB_BOOTSTRAP process. -->
<!-- ============================================================== -->
<dataSource id="fhirDefaultDefault" jndiName="jdbc/fhir_default_default" type="javax.sql.XADataSource" statementCacheSize="200" syncQueryTimeoutWithTransactionTimeout="true" validationTimeout="30s">
<jdbcDriver javax.sql.XADataSource="org.apache.derby.jdbc.EmbeddedXADataSource" libraryRef="sharedLibDerby"/>
<properties.derby.embedded createDatabase="create" databaseName="derby/fhirDB"/>
<connectionManager maxPoolSize="50" minPoolSize="10"/>
PostgreSQL

If you configure the FHIR server to use a PostgreSQL database, you must:

  1. create the database if it doesn’t already exist

  2. execute the fhir-persistence-schema utility with a db-type of postgresql to create the necessary schemas (tables, indices, functions, etc)

An executable fhir-persistence-schema jar can be downloaded from the project’s Releases tab and documentation can be found at https://github.com/LinuxForHealth/FHIR/tree/main/fhir-persistence-schema.

Since release 4.5.5 you can set the searchOptimizerOptions/from_collapse_limit and searchOptimizerOptions/join_collapse_limit properties to improve the performance of certain search queries involving multiple search parameters. This optimization is currently only available for PostgreSQL.

Citus

The LinuxForHealth FHIR Server includes experimental support for Citus (distributed PostgreSQL). The Citus implementation is designed to support greater scalability at the database layer by distributing FHIR resource data across multiple database nodes. See the schema design documentation here for details on how the data is distributed in a Citus database.

Currently, some FHIR search queries which follow references between resources such as _include, _revinclude and _has do not work. Support for these search queries may be included in a future update.

To use Citus:

  1. provision the database if it doesn’t already exist

  2. execute the fhir-persistence-schema utility with a db-type of citus to create the necessary schemas (tables, indices, functions, etc)

An executable fhir-persistence-schema jar can be downloaded from the project’s Releases tab and documentation can be found at https://github.com/LinuxForHealth/FHIR/tree/main/fhir-persistence-schema.

Since release 4.5.5 you can set the searchOptimizerOptions/from_collapse_limit and searchOptimizerOptions/join_collapse_limit properties to improve the performance of certain search queries involving multiple search parameters. This optimization is available for PostgreSQL and Citus.

Other

To enable the LinuxForHealth FHIR Server to work with other relational database systems, see https://linuxforhealth.github.io/FHIR/guides/BringYourOwnPersistence#adding-support-for-another-relational-database

3.3.1.2 Datastore configuration examples

To understand how the configuration properties are defined for one or more datastores, let’s start off with a couple of examples.

Example 1

Here is a simple example of a single (default) Derby datastore.

config/default/fhir-server-config.json

{
"fhirServer":{
"persistence":{
"factoryClassname":"org.linuxforhealth.fhir.persistence.jdbc.FHIRPersistenceJDBCFactory",
"datasources": {
"default": {
"type": "derby",
"currentSchema": "APP"

configDropins/overrides/datasource-derby.xml

<server>
<library id="fhirSharedLib">
<fileset dir="${shared.resource.dir}/lib/derby" includes="*.jar"/>
</library>
<!-- ============================================================== -->
<!-- TENANT: default; DSID: default; TYPE: read-write -->
<!-- ============================================================== -->
<dataSource id="fhirDefaultDefault" jndiName="jdbc/fhir_default_default" type="javax.sql.XADataSource" statementCacheSize="200" syncQueryTimeoutWithTransactionTimeout="true" validationTimeout="30s">

In this example, we define an embedded Derby database named derby/fhirDB (a location relative to the <WLP_HOME>/usr/servers/fhir-server directory). The datastore-id associated with this datastore is default, which is the value that is used if no X-FHIR-DSID request header is found in the incoming request. So, when only a single database is being used, it’s wise to leverage the default datastore-id value to allow REST API consumers to avoid having to set the X-FHIR-DSID request header on each request.

Example 2

This example shows a slightly more complex scenario. In this scenario, the acme tenant would like to store data in one of two study-specific PostgreSQL schemas with datastore-id values study1 and study2.

Furthermore, the REST API consumers associated with Acme applications will be coded to always set the X-FHIR-TENANT-ID request header to be acme and the X-FHIR-DSID request header to the specific datastore-id associated with each request (either study1 or study2). In this case, the following properties would be configured:

config/acme/fhir-server-config.json

{
"__comment":"Acme's FHIR server configuration",
"fhirServer":{
"persistence":{
"factoryClassname":"org.linuxforhealth.fhir.persistence.jdbc.FHIRPersistenceJDBCFactory",
"datasources": {
"study1": {
"type": "postgresql",

configDropins/overrides/datasources-acme.xml

<server>
<library id="fhirSharedLib">
<fileset dir="${shared.resource.dir}/lib/postgresql" includes="*.jar"/>
</library>
<!-- ============================================================== -->
<!-- TENANT: acme; DSID: study1; TYPE: read-write -->
<!-- ============================================================== -->
<dataSource id="fhirDatasourcePgAcmeStudy1" jndiName="jdbc/fhir_acme_study1" type="javax.sql.XADataSource" statementCacheSize="200" syncQueryTimeoutWithTransactionTimeout="true" validationTimeout="30s">

Note that because this example is using the default FHIR server naming scheme for datasource JNDI names, there is no need to include the ‘jndiName’ property in the fhir-server-config.json, although you can specify it should you wish to make the mapping clear.

Additionally, note that each datasource definition in the configDropin gets its own connection pool with properties defined by the ‘connectionManager’ element.

3.3.1.3 Database Access TransactionManager Timeout

The TransactionManager controls the timeout of database queries.

To modify the default transaction timeout value, set the environment variable FHIR_TRANSACTION_MANAGER_TIMEOUT or enter the value in the server.env file at the root of the WLP fhir-server instance. Example values are 120s (seconds) or 2m (minutes).

3.3.2 Payload Offload for Azure Blob

The LinuxForHealth FHIR Server can be configured to store the resource payload records in an Azure Blob container. Each record is stored as a JSON string with UTF-8 encoding. The LinuxForHealth FHIR Server relies on the blob service to compress/encrypt the data at rest. The blob service must apply the necessary security controls required when storing PHI, and connection to the service must use an encrypted transport.

3.3.2.1 Payload Offload Configuration for Azure Blob

To enable payload offloading using Azure Blob storage, complete the steps summarized below:

  1. Pick a container name to use for each tenant/datasource combination;
  2. Create a database.properties file with connection information for the FHIRSERVER user (not FHIRADMIN);
  3. Configure payload offloading in the main default/fhir-server-config.json file;
  4. Configure payload offloading in each tenant-specific fhir-server-config.json file;
  5. Create the container using the Azure Blob user interface, the Azure Blob API or the LinuxForHealth FHIR Server fhir-persistence-blob-app-*-cli.jar tool;
  6. (Optional) Periodically run the reconciliation tool to remove any orphan resource records from the offload datastore. See the fhir-persistence-blob-app project README for more information.

Take the following restrictions into account:

  1. Payload offloading is enabled at the server level. Offloading cannot be enabled/disabled on a per-tenant basis. If you want to support offloading for just one tenant, use a different LinuxForHealth FHIR Server instance;
  2. Payload offloading must be configured prior to ingesting any resource data;
  3. Payload offloading must not be disabled after resource data has been ingested;
  4. When payload offloading is enabled, FHIR resources are limited to 5000 MiB in size when rendered as uncompressed JSON. The practical limit is likely to be lower due to memory usage and typical socket and transaction timeouts.

3.3.2.2 Pick a Container Name

Each tenant/datasource combination requires its own container. Use a name that can be easily identified as belonging to the tenant and datasource, subject to the Azure Blob service naming restrictions.

3.3.2.3 Create the database.properties file

Create a properties file containing the RDBMS connection information. Note that the user should not be the FHIRADMIN user which is only used by the RDBMS schema creation tool. Use the database user configured in the LinuxForHealth FHIR Server datasource.xml file. Following the principle of least privilege access, this user typically has just the right set of privileges for the application to use objects in the FHIR data (fhirdata) schema:

db.host=localhost
db.port=5432
db.database=fhirdb
user=fhirserver
password=change-password
currentSchema=fhirdata

3.3.2.4 Add Payload Offload Configuration to default/fhir-server-config.json

In the main default/fhir-server-config.json, configure the fhirServer/persistence/factoryClassname as shown below and add a fhirServer/persistence/payload block containing the connection information for each datasource you have defined under fhirServer/persistence/datasources (typically there is just one datasource called default).

{
"__comment": "FHIR Server configuration",
"fhirServer": {
...
"persistence": {
"factoryClassname": "org.linuxforhealth.fhir.persistence.blob.FHIRPersistenceJDBCBlobFactory",
"datasources": {
"default": {
...

Container names allowed by Azure Blob are more restrictive than LinuxForHealth FHIR Server tenant and datasource names (for example they must be lower case and _ is not allowed - see the official documentation for more details). For this reason, the container name for each tenant and datasource must be specified in the fhirServer/persistence/payload/connectionProperties/containerName property.

3.3.2.5 Configure Payload Offloading Per Tenant

In each tenant fhir-server-config.json file, add a fhirServer/persistence/payload block containing the connection information for each datasource you have defined under fhirServer/persistence/datasources (typically there is just one datasource called default).

{
"__comment": "LinuxForHealth FHIR Server configuration",
"fhirServer": {
...
"persistence": {
"datasources": {
"default": {
...
}

3.3.2.6 Create the Container

The container can be created using the Azure Blob service or by running the following command:

java -jar fhir-persistence-blob-app-*-cli.jar \
--fhir-config-dir /path/to/wlp/usr/servers/defaultServer \
--tenant-id <tenant-id> \
--ds-id <ds-id> \
--create-container \
--no-dry-run

The container name will be read from the tenant’s fhir-server-config.json configuration, so it is important to complete that configuration step before running this command.

The command is designed to be idempotent - it checks first to see if the container already exists before attempting to create it. If the container is otherwise created after the exists check but before the create command is issued, the command will fail (this is a very small window).

3.3.2.7 Specifying Azure Blob Service Version [Optional]

To use an older version of the Azure Blob service API, specify a serviceVersion string in the connectionProperties element:

{
"__comment": "LinuxForHealth FHIR Server configuration",
"fhirServer": {
...
"persistence": {
...
"payload": {
"default": {
"__comment": "Azure Blob configuration for storing FHIR resource payload data",

3.4 “Update/Create” feature

Normally, the update operation is invoked with a FHIR resource which represents a new version of an existing resource. The resource specified in the update operation would contain the same id of that existing resource. If a resource containing a non-existent id were specified in the update invocation, an error would result.

The FHIR specification defines optional behavior for the update operation where it can create a new resource if a non-existent resource is specified in the invocation. The FHIR server supports this optional behavior via the fhirServer/persistence/common/updateCreateEnabled configuration parameter. If this configuration parameter is set to true (the default), then the update operation will create a new resource if it is invoked with a resource containing a non-existent id. If the option is set to false, then the optional behavior is disabled and an error would be returned.

The following example shows the JSON for enabling update operations to create resources:

{
"fhirServer":{
"persistence":{
"common":{
"updateCreateEnabled":true
}
}

4 Customization

You can modify the default server implementation by taking advantage of the LinuxForHealth FHIR Server’s extensibility. The following extension points are available:

  • Custom operations framework: The LinuxForHealth FHIR Server defines an operations framework that builds on the FHIR OperationDefinition resource in order to extend the FHIR REST API with custom endpoints.
  • Pluggable audit service: Logging and auditing options including Cloud Auditing Data Federation (CADF) over Apache Kafka.
  • Persistence interceptors: Intercept requests before and/or after each persistence action.
  • Resource validation: FHIRPath-based validation of FHIR resources on create or update with the ability to extend the system with custom constraints.

4.1 Extended operations

In addition to the standard REST API (create, update, search, and so forth), the LinuxForHealth FHIR Server supports the FHIR operations framework.

4.1.1 Packaged operations

The FHIR team provides implementations for the standard $validate, $document, $everything, $expand, $lookup, $subsumes, $closure, $export, $import, $convert, $apply and $translate operations, as well as a custom operation named $healthcheck, which queries the configured persistence layer to report its health.

The server also bundles $reindex to reindex instances of Resources so they are searchable, $retrieve-index to retrieve lists of resources available to be reindexed, and $erase to hard delete instances of Resources. To learn more about the $erase operation, read the design document.

To extend the server with additional operations, see Section 4.1.2 Custom operations

4.1.1.1 $validate

The $validate operation checks whether the attached content would be acceptable either generally, or as a create, update, or delete against an existing resource instance or type. By default, the $validate operation will validate a resource against the base specification and any profiles asserted in its Resource.meta.profile element. The default behavior may be changed in one of the following ways:

  • If a profile is specified via the optional profile parameter, the $validate operation will validate a resource against the base specification and the specified profile only. It will not validate against any other profiles asserted in the Resource.meta.profile element.
  • If the profile parameter is not specified, but the mode parameter is specified, and the mode parameter value is either create or update, the $validate operation will validate a resource against the base specification and any profiles asserted in its Resource.meta.profile element, but will do so based on profile configuration properties specified in the fhirServer/resources/<resourceType>/profiles section of the fhir-server-config.json file (see the Configuration properties reference for configuration details).

4.1.1.2 $healthcheck

The $healthcheck operation returns the health of the FHIR server and its datastore. In the default JDBC persistence layer, this operation creates a connection to the configured database and return its status. The operations returns 200 OK when healthy. Otherwise, it returns an HTTP error code and an OperationOutcome with one or more issues.

4.1.2 Custom operations

In addition to the provided operations, the FHIR server supports user-provided custom operations through a Java Service Provider Interface (SPI).

To contribute an operation:

  1. Implement each operation as a Java class that extends org.linuxforhealth.fhir.operation.AbstractOperation from fhir-operation.jar. Ensure that your implementation returns an appropriate OperationDefinition in its getDefinition() method, because the framework validates both the request and response payloads to ensure that they conform to the definition.

  2. Create a file named org.linuxforhealth.fhir.operation.FHIROperation with one or more fully qualified FHIROperation classnames and package it in your jar under META-INF/services/.

  3. Include your jar file under the <WLP_HOME>/usr/servers/fhir-server/userlib/ directory of your installation.

  4. Restart the FHIR server. Changes to custom operations require a server restart, because the server discovers and instantiates operations during server startup only.

After you register your operation with the server, it is available via HTTP POST at [base]/api/1/$<yourCode>, where <yourCode> is the value of your OperationDefinition’s code.

4.2 Notification Service

The FHIR server provides a notification service that publishes notifications about persistence events, specifically create, update, and delete operations. The notification service can be used by other components to trigger specific actions that need to occur as resources are being updated in the FHIR server datastore.

The notification service supports two implementations: WebSocket and Kafka.

4.2.1 FHIRNotificationEvent

The FHIRNotificationEvent class defines the information that is published by the notification service. Each notification event published to the WebSocket or Kafka topic is an instance of FHIRNotificationEvent, serialized as a JSON object. This JSON object will have the following fields:

Field nameTypeDescription
operationTypeStringThe operation associated with the notification event. Valid values are create and update.
locationStringThe location URI of the resource associated with the notification event. To retrieve this resource, invoke a GET request using the location URI value as the URL string.
lastUpdatedStringThe date and time of the last update made to the resource associated with the notification event.
resourceIdStringThe logical id of the resource associated with the notification event.
resourceStringA stringified JSON object which is the resource associated with the notification event.
tenantIdStringThe tenant that generated this notification
datasourceIdStringThe datasource used by the tenant

The following JSON is an example of a serialized notification event:

{
"lastUpdated":"2016-06-01T10:36:23.232-05:00",
"location":"Observation/3859/_history/1",
"operationType":"create",
"resourceId":"3859",
"tenantId":"default",
"datasourceId":"default",
"resource":{ …<contents of resource>… }
}

If the resource is over the limit specified in fhirServer/notifications/common/maxNotificationSizeBytes, the default value is to subset id, meta, resourceType, and all Resource required fields and add the subset to the FHIRNotificationEvent. In alternative configurations, user may set fhirServer/notifications/common/maxNotificationSizeBehavior to omit and subsequently retrieve the resource using the location.

4.2.2 WebSocket

The WebSocket implementation of the notification service will publish notification event messages to a WebSocket. To enable WebSocket notifications, set the fhirServer/notifications/websocket/enabled property to true, as in the following example:

{
"fhirServer":{
"notifications":{
"websocket":{
"enabled":true
}

The WebSocket location URI is ws://<host>:<port>/fhir-server/api/v4/notification, where <host> and <port> represent the host and port of the FHIR server’s REST API endpoint. So for example, if the FHIR server endpoint’s base URL is https://localhost:9443/fhir-server/api/v4 then the corresponding location of the WebSocket would be ws://localhost:9443/fhir-server/api/v4/notification.

4.2.3 Kafka

The Kafka implementation of the notification service will publish notification event messages to a Kafka topic. To configure the Kafka notification publisher, configure properties in the fhir-server-config.json file as indicated in the following example:

{
"fhirServer":{
"notifications":{
"kafka":{
"enabled":true,
"topicName":"fhirNotifications",
"connectionProperties":{

The fhirServer/notifications/kafka/enabled property is used to enable or disable the Kafka publisher component.

The fhirServer/notifications/kafka/topicName property is used to configure the appropriate topic name to which the notification events should be published.

The fhirServer/notifications/kafka/connectionProperties property group is used to configure the properties necessary to successfully connect to the Kafka server. You can specify an arbitrary group.id. The bootstrap.servers property is required, but the rest are optional, although if your Kafka server is configured to require an SSL connection and client authentication, then the remaining properties must also be set. For more details about Kafka-related properties, see the Kafka documentation.

In the connectionProperties property group in preceding example, you’ll notice that the password-related properties have encoded values. To store a value requiring security (such as a password), you can use Liberty’s securityUtility command to encode the value. See Section 3.1 Encoded passwords for details.

Before you enable Kafka notifications, it’s important to understand the topology of the environment in which the FHIR server instance will be running. Your topic name selection should be done in consideration of the topology. If you have multiple instances of the FHIR server clustered together to form a single logical endpoint, then each of those instances should be configured to use the same Kafka topic for notifications. This is so that notification consumers (subscribers) can subscribe to a single topic and receive all the notifications published by each of the FHIR server instances within the cluster.

On the other hand, if you have two completely independent FHIR server instances, then you should configure each one with its own topic name.

The FHIRNotificationEvent is asynchronous by default. If you want to specify a synchronous request, you can set fhirServer/notifications/kafka/sync to true, which ensures no message is lost in publishing, however it does add latency in each request.

4.2.3 NATS

The NATS implementation of the notification service publishes notification event messages to a NATS streaming cluster. To configure the NATS notification publisher, configure properties in the fhir-server-config.json file as shown in the following example:

{
"fhirServer":{
...
"notifications":{
...
"nats": {
"enabled": true,
"cluster": "nats-streaming",
"channel": "fhirNotifications",

Set the fhirServer/notifications/nats/enabled property to true and provide the name of your NATS cluster for the value of fhirServer/notifications/nats/cluster. You may leave fhirServer/notifications/nats/channel and fhirServer/notifications/nats/clientId as defined. Provide the URL for one or more NATS servers as the value for fhirServer/notifications/nats/servers.

To use TLS to connect to your NATS cluster, set fhirServer/notifications/nats/useTLS to true and provide client truststore and keystore locations and passwords as the remaining config values. Ensure that your NATS cluster is configured for TLS client connections.

To store a value requiring security, such as a password, use Liberty’s securityUtility command to encode the value. See Section 3.1 Encoded passwords for details.

4.2.4 Resource type filtering

By default, notification messages are published for all create and update persistence operations. However, the FHIR server allows you to configure a list of resource types for which notification events will be published. To do this, list the resource types for which you want to generate notifications in an array of strings within the fhirServer/notifications/common/includeResourceTypes property in the fhir-server-config.json file, as in the following example:

{
"fhirServer":{
"notifications":{
"common":{
"includeResourceTypes":[
"Observation",
"Patient"

With the includeResourceTypesproperty set as in the preceding example, the FHIR server publishes notification events only for Patient and Observation resources. If you omit this property or set its value to [] (an empty array), then the FHIR server publishes notifications for all resource types.

4.3 Persistence interceptors

The LinuxForHealth FHIR Server supports a persistence interceptor feature that enables users to add their own logic to the REST API processing flow around persistence events. This can be used to enforce application-specific business rules associated with resources. Interceptor methods are called immediately before or after each persistence operation.

4.3.1 FHIRPersistenceInterceptor interface

A persistence interceptor implementation must implement the org.linuxforhealth.fhir.server.spi.interceptor.FHIRPersistenceInterceptor interface.

Each interceptor method receives a parameter of type FHIRPersistenceEvent, which contains context information related to the request being processed at the time that the interceptor method is invoked. It includes the FHIR resource, security information, request URI information, and the collection of HTTP headers associated with the request.

There are many use cases for persistence interceptors:

  1. Enforce certain application-specific governance rules, such as making sure that a patient has signed a consent form prior to allowing his/her data to be persisted. For example, the beforeCreate and beforeUpdate methods could verify that the patient has a consent agreement on file and, if not, then throw a FHIRPersistenceInterceptorException to prevent the create or update events from completing. The exception thrown by the interceptor method should include one or more OperationOutcome issues and these issues will be added to an OperationOutcome in the REST API response. The HTTP status code of the response will be determined by the IssueType of the first issue in the list.

  2. Perform additional access control. For example, beforeSearch can be used to alter the incoming SearchContext (e.g. by adding additional search parameters). Similarly afterRead, afterVRead, afterHistory, and afterSearch can be used to verify that the end user is authorized to access the resources before they are returned.

It is also possible to modify the incoming resources from the beforeCreate and beforeUpdate methods. For example, an interceptor could be used to add tags to resources on their way into the server. However, it is important to realize that interceptors are called after resource validation. Therefore, interceptor authors must be careful not to alter the resources in a way that breaks conformance with the profiles claimed in Resource.meta.profile or the secondary constraints in the specification. When in doubt, interceptors that modify the incoming resource can use the FHIRValidator to re-validate the resource(s) after they are altered.

4.3.2 Implementing a persistence interceptor

To implement a persistence interceptor, complete the following steps:

  1. Develop a Java class which implements the FHIRPersistenceInterceptor interface.

  2. Store the fully-qualified classname of your interceptor implementation class in a file called :

    META-INF/services/org.linuxforhealth.fhir.server.spi.interceptor.FHIRPersistenceInterceptor

    Here’s an example of the file contents:

    com.example.mysolution.MyInterceptor

  3. Copy your jar to the <WLP_HOME>/usr/servers/fhir-server/userlib directory so that it is accessible to the FHIR server via the classpath (the server.xml file contains a library element that defines this directory as a shared library).

  4. Re-start the FHIR server.

4.4 Registry resources

The LinuxForHealth FHIR Server includes a dynamic registry of conformance resources. The server pre-packages conformance artifacts from HL7 FHIR version 4.3.0 and uses a Java ServiceLoader to discover additional registry resource providers on the classpath.

The server consults this registry for:

  • StructureDefinition, ValueSet, and CodeSystem resources for resource validation.
  • SearchParameter and CompartmentDefinition resources for search.
  • ValueSet and CodeSystem resources for terminology operations.
  • And more.

One common technique for extending FHIR with a set of conformance resources is to build or reference an Implementation Guide.

The LinuxForHealth FHIR Server includes a PackageRegistryResourceProvider for registering implementation guide resources.

Additionally, we pre-package a number of popular implementation guides and make those available from both our GitHub Releases and Maven Central.

Finally, the LinuxForHealth FHIR Server includes a built-in ServerRegistryResourceProvider that can be used to bridge conformance resources from the tenant data store (uploaded through the REST API) to the registry. This provider can be enabled/disabled via the fhirServer/core/serverRegistryResourceProviderEnabled property, but we recommend leaving it disabled for performance-intensive workloads.

4.5 Resource validation

As mentioned in the previous section, the LinuxForHealth FHIR Server registry is consulted during resource validation.

4.5.1 HL7 spec-defined validation support

The FHIR specification provides a number of different validation resources including:

  1. XML Schemas
  2. ISO XML Schematron rules
  3. Structure Definitions / Profiles for standard resource types, data types and built-in value sets

The FHIR server validates incoming resources for create and update interactions using the resource definitions and their corresponding FHIRPath constraints. Additionally, the FHIR server provides the $validate operation that API consumers can use to POST resources and get validation feedback:

POST <base>/<resourceType>/$validate

4.5.2 Extension validation

FHIR resources can be extended. Each extension has a url and servers can use these urls to validate the contents of the extension.

The LinuxForHealth FHIR Server performs extension validation by looking up the extension definition in its internal registry. If an instance contains extensions that are unknown to the server, then the server will include a validation warning that indicates this extension could not be validated.

4.5.3 Profile validation

The LinuxForHealth FHIR Server can be extended with custom profile validation. This allows one to apply validation rules on the basis of the Resource.meta.profile values included on the resource instance.

For example, you can configure a set of FHIRPath Constraints to run for resources that claim conformance to the http://example.com/fhir/profile/partner profile when you see an input resource like the following:

{
"resourceType" : "Patient",
"meta": {
"profile": [ "http://example.com/fhir/profile/partner" ]
},
"name" : [ {
"family" : [ "Doe" ],
"given" : [ "John" ]
} ],

The following configuration parameters can be used to specify rules relating to the set of profiles that are specified in a resource’s meta.profile element:

  • fhirServer/resources/<resourceType>/profiles/atLeastOne - to specify a set of profiles, at least one of which a resource must claim conformance to and be successfully validated against in order to be persisted to the FHIR server.
  • fhirServer/resources/<resourceType>/profiles/notAllowed - to specify a set of profiles to which a resource is not allowed to claim conformance.
  • fhirServer/resources/<resourceType>/profiles/allowUnknown - to indicate whether a warning or an error is issued if a profile specified in a resource’s meta.profile element is not loaded in the FHIR server. The default value is true, meaning unknown profiles are allowed to be specified. The profile will be ignored and just a warning will be returned. If set to false, this means unknown profiles are not allowed to be specified. An error will be returned and resource validation will fail.
  • fhirServer/resources/<resourceType>/profiles/defaultVersions - to specify which version of a profile will be used during resource validation if the profile specified in a resource’s meta.profile element does not contain a version. If a default profile version is not configured using this configuration parameter for an asserted profile, the FHIR server will determine the default version to use for validation.

Before calling the FHIR validator to validate a resource against the set of profiles specified in its meta.profile element that it is claiming conformance to, the following pre-validation will be performed for that set of profiles based on the configuration parameters listed above:

  1. If any specified profile does not contain a version, and that profile is in the set of profiles configured to have a default version via the fhirServer/resources/<resourceType>/profiles/defaultVersions configuration parameter, the default version for that profile will be appended to the profile name, and it is this new profile name containing the version which will be evaluated against in the following steps.
  2. If the fhirServer/resources/<resourceType>/profiles/notAllowed configuration parameter is set to a non-empty list, an error will be returned for any specified profile that is in the list, and validation will fail.
  3. If the fhirServer/resources/<resourceType>/profiles/allowUnknown configuration parameter is set to false, an error will be returned for any specified profile that is not loaded in the FHIR server, and validation will fail.
  4. If the fhirServer/resources/<resourceType>/profiles/atLeastOne configuration parameter is set to a non-empty list, an error will be returned if none of the specified profiles is in the list, and validation will fail.

If the resource passes pre-validation successfully, it will then be passed to the FHIR validator to validate conformance to the specified set of profiles.

The following example configuration shows how to define these configuration parameters:

{
"fhirServer":{
"resources":{
"open": true,
"Observation": {
"profiles": {
"atLeastOne": [
"http://example.com/fhir/profile/partnerA",

Given this configuration, in order for an Observation resource to be persisted to the FHIR server:

  • The resource’s meta.profile element must specify either the http://example.com/fhir/profile/partnerA profile or the http://example.com/fhir/profile/partnerB|1.0 profile or both, based on the fhirServer/resources/Observation/profiles/atLeastOne list. Other profiles may be specified as well assuming they pass the following checks.
  • The resource’s meta.profile element must not specify any profile which is specified in the fhirServer/resources/Resource/profiles/notAllowed list. Since the notAllowed property is not specified in the fhirServer/resources/Observation/profiles section, it is inherited from the fhirServer/resources/Resource/profiles section if specified there.
  • The resource’s meta.profile element must not specify any profile which is not loaded in the FHIR server, based on the fhirServer/resources/Observation/profiles/allowUnknown value of false.
  • The resource must successfully validate against all specified profiles. Note that if the http://example.com/fhir/profile/partnerA profile is specified, what is actually evaluated against and eventually passed to the FHIR validator is http://example.com/fhir/profile/partnerA|1.1. This is because the http://example.com/fhir/profile/partnerA profile is specified in the fhirServer/resources/Observation/profiles/defaultVersions set with a default version of 1.1.

In order for a Patient resource to be persisted to the FHIR server:

  • The resource’s meta.profile element is not required to specify any profile since the atLeastOne property is not specified in the fhirServer/resources/Patient/profiles section, nor is it specified in the fhirServer/resources/Resource/profiles section, where the property would be inherited from if specified. Any valid Patient profile may be specified assuming it passes the following checks.
  • The resource’s meta.profile element cannot specify either the http://example.com/fhir/profile/partnerC profile or the http://example.com/fhir/profile/partnerD|2.0 profile, based on the fhirServer/resources/Patient/profiles/notAllowed list.
  • The resource’s meta.profile element may specify a profile which is not loaded in the FHIR server. Based on the absence of the allowUnknown property in the fhirServer/resources/Patient/profiles section, as well as the absence of that property in the fhirServer/resources/Resource/profiles section (where the property would be inherited from if specified), the default value of true is used. This means unknown profiles (not loaded in the FHIR server) will be allowed and will simply be ignored.
  • The resource must successfully validate against all specified profiles. Note that since the defaultVersions property is not specified in the fhirServer/resources/Patient/profiles section, this property will be inherited from the fhirServer/resources/Resource/profiles/defaultVersions property. So if a profile is specified in the resource’s meta.profile element that is in the set of defaultVersions profiles, what will actually be evaluated against and eventually passed to the FHIR validator is the original profile name with its specified default version appended to it.

If a profile in either the list specified by the fhirServer/resources/<resourceType>/profiles/atLeastOne configuration parameter or the list specified by the fhirServer/resources/<resourceType>/profiles/notAllowed configuration parameter contains a version, for example http://example.com/fhir/profile/partner|1.0, then a profile of the same name specified in the resource’s meta.profile element will only be considered a match if it contains exactly the same version. However, if a profile in the lists specified by the configuration parameters does not contain a version, for example http://example.com/fhir/profile/partner, then a profile of the same name specified in the resource’s meta.profile element will be considered a match whether it contains a version or not.

Keep in mind that a profile name specified in the resource’s meta.profile element could be modified due to the resource’s fhirServer/resources/<resourceType>/profiles/defaultVersions configuration. It is this modified profile name that is used in the matching process and in the resource’s validation, but only for those purposes. The meta.profile element of the original resource itself is not updated with the modified profile name.

Using the example configuration above for the Observation resource type, if the profile http://example.com/fhir/profile/partnerA|3.2 was specified in a resource’s meta.profile element then it would be considered a match for the http://example.com/fhir/profile/partnerA profile specified in the fhirServer/resources/Observation/profiles/atLeastOne list. Conversely, if the profile http://example.com/fhir/profile/partnerB was specified in the resource’s meta.profile element then it would not be considered a match for the http://example.com/fhir/profile/partnerB|1.0 profile specified in the fhirServer/resources/Observation/profiles/atLeastOne list.

The LinuxForHealth FHIR Server pre-packages all conformance resources from the core specification.

See Validation Guide - Optional profile support for a list of pre-built Implementation Guide resources and how to load them into the LinuxForHealth FHIR Server.

See Validation Guide - Making profiles available to the fhir registry for information about how to extend the server with additional Implementation Guide artifacts.

In addition to supporting tenant-specific search parameter extensions as described in Section 3.2.2 Tenant-specific configuration properties, the LinuxForHealth FHIR Server also supports loading search parameters from the registry.

For performance reasons, the registry search parameters are retrieved once and only once during startup.

The set of search parameters can filtered / refined via fhirServer/resources/[resourceType]/searchParameters as described in the Search configuration guide.

4.7 FHIR client API

4.7.1 Overview

In addition to the server, we also offer a Java API for invoking FHIR REST APIs. The LinuxForHealth FHIR Client is built on JAX-RS 2.1 and provides a simple properties-driven client that can be configured for a given endpoint, mutual authentication, request/response logging, and more.

4.7.2 Maven coordinates

To use the FHIR Client from your application, specify the fhir-client artifact as a dependency within your pom.xml file, as in the following example:

<dependency>
<groupId>org.linuxforhealth.fhir</groupId>
<artifactId>fhir-client</artifactId>
<version>${fhir.client.version}</version>
</dependency>

4.7.3 Client properties

Applicable client properties are documented in the FHIRClient interface. Below is a summary of the most pertinent ones:

PropertyDefaultDescription
fhirclient.rest.base.url*The target FHIR Server’s base URL
fhirclient.default.mimetypeapplication/fhir+json; fhirVersion=4.3The value to use in the HTTP headers (Accept and Content-Type) passed to the FHIR Server.
fhirclient.truststore.locationThe client truststore’s filename. The client truststore contains the server’s public key certificates and is used to verify the server’s identity.
fhirclient.truststore.passwordThe client truststore’s password.
fhirclient.hostnameVerification.enabledtrueIndicates whether or not to enable hostname verification when connecting over TLS.
fhirclient.basicauth.enabledfalseIndicates whether Basic Authentication should be used. If enabled, then the username and password properties are required.
fhirclient.basicauth.usernameThe username to use with Basic Authentication.
fhirclient.basicauth.passwordThe password to use with Basic Authentication.
fhirclient.clientauth.enabledfalseIndicates whether mutual TLS certificate-based authentication should be used. If enabled, then keystore properties are required.
fhirclient.keystore.locationThe client keystore’s filename. The client keystore constains the client’s public/private key pair. When using client certificate-based authentication, this is now the client supplies its identity to the server
fhirclient.keystore.passwordThe client keystore’s password.
fhirclient.keystore.key.passwordThe password associated with the client’s certificate within the keystore.
fhirclient.logging.enabledfalseWhether to enable request/response logging (useful for debug).
fhirclient.http.receive.timeout130000 (130 seconds)The time, in seconds, to wait for a server response.

4.7.4 Sample usage

For examples on how to use the LinuxForHealth FHIR Client, look for tests like org.linuxforhealth.fhir.client.test.mains.FHIRClientSample from the fhir-client project in git. Additionally, the FHIR Client is heavilly used from our integration tests in fhir-server-test.

4.8 Using local references within request bundles

Inter-dependencies between resources are typically defined by one resource containing a field of type Reference which contains an external reference5 to another resource. For example, an Observation resource could reference a Patient resource via the Observation’s subject field. The value that is stored in the Reference.reference field (for example, Observation.subject.reference in the case of the Observation resource) could be an absolute URL, such as https://fhirserver1:9443/fhir-server/api/v4/Patient/12345, or a relative URL, such as Patient/12345.

As described above, in order to establish a reference to a resource, you must first know its resource identifier. However, if you are using a request bundle to create both the referenced resource (Patient in this example) and the resource which references it (Observation), then it is impossible to know the Patientresource identifier before the request bundle has been processed (that is, before the new Patient resource is created).

Thankfully, the HL7 FHIR specification defines a way to express a dependency between two resources within a request bundle by using a local identifier to identify the resource being referenced, and a local reference6 to reference the resource via its local identifier. In the following example, a request bundle contains a POST request to create a new Patient resource, along with a POST request to create a new Observation resource that references that Patient:

{
"resourceType": "Bundle",
"type": "batch",
"entry" : [ {
"fullUrl" : "urn:uuid:7113a0bb-d9e0-49df-9855-887409388c69",
"resource" : {
"resourceType" : "Patient",
},

To define a local identifier for a resource, you must specify it in the Bundle.entry.fullUrl field of the resource’s bundle entry. The HL7 FHIR specification recommends that the local identifier be the persistent identity of the resource if known, otherwise a UUID value prefixed with urn:uuid: as in the preceding example. However, the FHIR server does not require the use of a UUID value. You can use any fullUrl value you like as long as it is unique within the bundle. For example, you can use urn:Patient_1, urn:ABC, or urn:Foo.

After you define a local identifier for the referenced resource, you can then define one or more references to that resource by using the local identifier instead of an external identifier. In the preceding example, you can see that the Observation’s subject.reference field specifies the Patient’s local identifier as specified in the fullUrl field of the Patient’s request entry.

4.8.1 Processing rules

The following processing rules apply for the use of local references within a request bundle:

  1. A local identifier must be defined via a request bundle entry’s fullUrl field in order for that local identifier to be used in a local reference.

  2. Local references will only be recognized for local identifiers associated with request bundle entries with a request method of POST or PUT.

  3. POST requests will be processed before PUT requests.

  4. There is no order dependency within a request bundle for bundle entries defining local identifiers and bundle entries which reference those local identifiers via local references.
  5. If a resource in a request bundle entry contains a field of type `Reference` having a value which is a relative URL, and if that bundle entry has a local identifier (`fullUrl`) which is an absolute URL conforming to the FHIR specification's [RESTful URL definition](https://hl7.org/fhir/R4B/references.html#regex), then the FHIR server will attempt to resolve the local reference as follows, based on the [FHIR specification](https://hl7.org/fhir/R4B/bundle.html#references): - it will extract the FHIR base URL from the local identifier and append the local reference to it - it will then try to resolve the reference within the request bundle using the updated local reference

    See the relative local reference example below for an illustration of this rule.

In the example above, you can see that there are two POST requests and the Patient request entry appears in the bundle before the Observation request entry. However, based on the order dependency processing rule, it would still be a valid request bundle even if the Observation request entry appeared before the Patient request entry.

The following examples also satisfy the local reference processing rules:

Example: Circular references

{
"resourceType" : "Bundle",
"type" : "batch",
"entry" : [ {
"fullUrl" : "urn:Encounter_1",
"resource" : {
"resourceType" : "Encounter",
"reasonReference" : [ {

While processing a request bundle, but before processing individual request entries, the LinuxForHealth FHIR Server detects the use of a local identifier within any POST or PUT request entry’s fullUrl field, and establishes a mapping between that local identifier and the corresponding external identifier that results from performing the POST or PUT operation.

Using the circular reference example above, the FHIR server detects the use of local identifiers in the Encounter request entry (urn:Encounter_1) and in the Procedure request entry (urn:Procedure_1), and establishes a mapping between the local identifiers and the external references to be associated with the new Encounter and Procedure resources (for example, Encounter/1cc5d299-d2be-4f93-8745-a121232ffe5b and Procedure/22b21fcf-8d00-492d-9de0-e25ddd409eaf).

Then when the FHIR server processes the POST requests for the Encounter and Procedure resources, it detects the use of the local references and substitutes the corresponding external references for them before creating the new resources. Below is the response bundle for the request bundle in the circular references example. We can see that the Encounter’s reasonReference.reference field now contains a proper external reference to the newly-created Procedure resource, and the Procedure’s encounter.reference field now contains a proper external reference to the newly-created Encounter resource:

{
"resourceType" : "Bundle",
"type" : "batch-response",
"entry" : [ {
"resource" : {
"resourceType" : "Encounter",
"id" : "1cc5d299-d2be-4f93-8745-a121232ffe5b",
"reasonReference" : [ {

Example: Reference to entry with conditional create

{
"resourceType" : "Bundle",
"type" : "batch",
"entry" : [ {
"resource" : {
"resourceType" : "Observation",
"id" : "25b1fe08-7612-45eb-af80-7e15d9806b2b",
"subject" : {

In the above example, even though the Patient request entry is a conditional create request, this is still a valid request bundle, because the FHIR server resolves any conditional requests before it establishes the mapping between local identifiers and the corresponding external identifiers that will result from performing the POST or PUT operation.

Example: Reference via relative local reference

{
"resourceType" : "Bundle",
"type" : "batch",
"entry" : [ {
"fullUrl" : "https://fhirserver1:9443/fhir-server/api/v4/Patient/new",
"resource" : {
"resourceType" : "Patient",
},

In this example, we demonstrate the relative reference processing rule. The local identifiers for the request bundle entries (https://fhirserver1:9443/fhir-server/api/v4/Patient/new and https://fhirserver1:9443/fhir-server/api/v4/Observation/new) are absolute URLs that conform to the FHIR specification’s RESTful URL definition . When the FHIR server attempts to resolve the Observation request entry’s subject reference (Patient/new), it will apply the processing rule for relative references, since the reference is a relative URL. The subject reference will be modified to be the original local reference (Patient/new) appended to the FHIR base URL extracted from the Observation entry’s local identifier (https://fhirserver1:9443/fhir-server/api/v4/). The resulting local reference (https://fhirserver1:9443/fhir-server/api/v4/Patient/new) will then be a valid reference to the Patient request bundle entry.

4.9 Multi-tenancy

The FHIR server includes features that allow a single instance of the server to simultaneously support multiple tenants. A tenant is defined as a group of one or more FHIR REST API consumers that share a FHIR server configuration along with one or more data stores associated with that configuration. A tenant could be a single application using the FHIR REST API, or it could be a group of applications belonging to a single customer. The main idea behind multi-tenancy is that each tenant can experience its own customized FHIR server runtime behavior and its data can be physically isolated from other tenants’ data for increased security and privacy.

4.9.1 Specifying the tenant id

To support multi-tenancy, the FHIR server must know which tenant an incoming REST API request is intended for. To provide the tenant id to the FHIR server, a REST API consumer must set a request header in each REST API request. The name of this request header is itself configurable by setting the fhirServer/core/tenantIdHeaderName configuration property in the FHIR server’s global configuration file (located at $⁠{server.config.dir}/config/default/fhir-server-config.json). The following example shows the default setting for this configuration parameter:

{
"fhirServer":{
"core":{
"tenantIdHeaderName":"X-FHIR-TENANT-ID"
},
}
}

With this configuration in place, each REST API consumer would need to set the X-FHIR-TENANT-ID request header to the appropriate tenant id. Each tenant’s tenant id value is assigned by the deployer. It is simply a short name associated with the tenant and must be unique among all tenants supported by a single FHIR server instance. For example, let’s suppose Acme Healthcare, Inc. is using the FHIR server and their tenant id has been assigned by the deployer as “acme”. In this case, Acme-related applications would set the following request header in each REST API request: X-FHIR-TENANT-ID: acme

As mentioned earlier, the name of the request header is configurable in the FHIR server’s global configuration file. For example, the FHIR server deployer could configure the request header name to be X-WHCLSF-tenant-id by setting tenantIdHeaderName as shown in the following example:

{
"fhirServer":{
"core":{
"tenantIdHeaderName":"X-WHCLSF-tenant-id"
},
}
}

This would be useful in an environment where the applications might already be using a similar type of request header. With this configuration in place, the “Acme Healthcare, Inc.” tenant would set the following request header in each REST API request: X-WHCLSF-tenant-id: acme

4.9.2 Configuration properties

The FHIR server allows a deployer to configure a subset of the supported configuration properties on a tenant-specific basis. For a complete list of configuration properties supported on a per-tenant basis, see Section 5.1.3 Property attributes.

When the FHIR server needs to retrieve any of the tenant-specific configuration properties, it does so dynamically each time the property value is needed. This means that a deployer can change the value of a tenant-specific property within a tenant’s configuration file on disk, and the FHIR server will immediately “see” the new value the next time it tries to retrieve it. For example, suppose the deployer initially defines the acme tenant’s fhir-server-config.json file such that the fhirServer/core/defaultPrettyPrint property is set to true.

Requests from the acme tenant would result in pretty-printed responses (with newlines and indentation), making it easier for humans to read. Now suppose the deployer changes the value of that property to true within the acme tenant’s fhir-server-config.json file. A subsequent REST API request would then see the output condensed into a single line with minimal whitespace.

4.9.2.1 Examples

This section contains examples of both a global (default) configuration and a tenant-specific configuration.

Global configuration (default)

The global configuration contains non-tenant specific configuration parameters (configuration parameters that are not resolved or used on a tenant-specific basis), as well as default values for tenant-specific configuration parameters.

${server.config.dir}/config/default/fhir-server-config.json

{
"__comment":"FHIR server global (default) configuration",
"fhirServer":{
"core":{
"defaultPrettyPrint":false,
"tenantIdHeaderName":"X-FHIR-TENANT-ID"
},
"notifications":{
"common":{
Acme Healthcare, Inc. (acme)

The Acme Healthcare, Inc tenant configuration overrides the fhirServer/core/defaultPrettyPrint property so that the development team can more easilly read the messages.

${server.config.dir}/config/acme/fhir-server-config.json

{
"__comment":"FHIR server configuration for tenant: Acme Healthcare, Inc.",
"fhirServer":{
"core":{
"defaultPrettyPrint":true
}
}
}

It is also possible to configure the persistence properties for a specific tenant, for example to set an alternate database hostname or database schema name.

4.10 Bulk data operations

The LinuxForHealth FHIR Server implements bulk data export according to the HL7 FHIR BulkDataAccess IG: STU1, and bulk data import is implemented according to the Proposal for $import Operation.

There are 2 modules involved:

  • fhir-operation-bulkdata
  • fhir-bulkdata-webapp

The fhir-operation-bulkdata module implements the REST APIs for bulk data export, import and status as FHIR Operations. There are five operations:

OperationPath
ExportOperationsystem $export
PatientExportOperationPatient Patient/$export
GroupExportOperationGroup Group/[id]/$export
ImportOperationimport resources using the system endpoint, $import
StatusOperationpolling status for import and export $bulkdata-status

Each operation queues a job with the Open Liberty JavaBatch framework. Each job instance unit-of-work is executed as a job with the fhir-bulkdata-webapp module. There are 5 JavaBatch jobs defined in the fhir-bulkdata-webapp module for the above 3 export operations and 1 import operation:

Java Batch JobOperation
FhirBulkExportChunkJob$export
FhirBulkExportFastJob$export
FhirBulkExportPatientChunkJobPatient/$export
FhirBulkExportGroupChunkJobGroup/[id]/$export
FhirBulkImportChunkJob$import

The fhir-bulkdata-webapp module is a wrapper for the whole BulkData web application, which is the build artifact - fhir-bulkdata-webapp.war. This web archive is copied to the apps/ directory of the liberty server. The feature is configured using the configDropins/default/bulkdata.xml, such as:

<webApplication id="fhir-bulkdata-webapp" location="fhir-bulkdata-webapp.war" name="fhir-bulkdata-webapp">
<classloader privateLibraryRef="configResources,fhirUserLib"/>
<application-bnd>
<security-role id="users" name="FHIRUsers">
<group id="bulkUsersGroup" name="FHIRUsers"/>
</security-role>
</application-bnd>
</webApplication>

The Bulk Data web application writes the exported FHIR resources to an IBM Cloud Object Storage (COS), any Amazon S3-Compatible bucket (e.g, Amazon S3, minIO etc), or directory as configured in the per-tenant server configuration under fhirServer/bulkdata. The following is an example configuration for bulkdata; please refer to section 5 for the detailed description of these properties:

"bulkdata": {
"enabled": true,
"core": {
"api": {
"url": "https://localhost:9443/ibm/api/batch",
"user": "fhiradmin",
"password": "change-password",
"truststore": "resources/security/fhirTrustStore.p12",
"truststorePassword": "change-password"

Each tenant’s configuration may define multiple storageProviders. The default is assumed, unless specified with the X-FHIR-BULKDATA-PROVIDER and X-FHIR-BULKDATA-PROVIDER-OUTCOME. Each tenant’s configuration may mix the different providers, however each provider is only of a single type. For instance, minio is aws-s3 and default is file. Note, type http is only applicable to $import operations. Export is only supported with s3 and file.

To use Amazon S3 bucket for exporting, please set accessKeyId to S3 access key, and set secretAccessKey to the S3 secret key, and the auth type to hmac.

Basic system exports to S3 without typeFilters use a streamlined implementation which bypasses the LinuxForHealth FHIR Server Search API for direct access to the data enabling better throughput. The fhirServer/bulkdata/core/systemExportImpl property can be used to disable the streamlined system export implementation. To use the legacy implementation based on LinuxForHealth FHIR Server search, set the value to “legacy”. The new system export implementation is used by default for any export not using typeFilters. Exports using typeFilters use FHIR Search, and cannot use the streamlined export.

To import using the $import operation with https, one must additionally configure the fhirServer/bulkdata/storageProviders/(source)/validBaseUrls. For example, if one stores bulk data at https://test-url1.cos.ibm.com/bucket1/test.ndjson and https://test-url2.cos.ibm.com/bucket2/test2.ndjson you must specify both baseUrls in the configuration:

"validBaseUrls": [
"https://test-url1.cos.ibm.com/bucket1",
"https://test-url2.cos.ibm.com/bucket2"
]

These base urls are not checked when using cloud object store and bulk-import. If you need to disable the validBaseUrls feature you may add fhirServer/bulkdata/storageProviders/(source)/disableBaseUrlValidation as true.

For Bulk Data import, the fhirServer/bulkdata/core/maxInputs is used to configure a maximum number of inputs supported by the instance. The default number is 5. There is a hard character limit on the total input type and url must be under 4096 characters, as such the configuration may be tuned for each url scheme.

Note: When $import is executed, if a resource to import includes a Resource.id then this id is honored (via create-on-update). If Resource.id is not valued, the server will perform a create and assign a new Resource.id for this resource.

Following is the beautified response of sample polling location request after the export is finished:

{
"transactionTime": "2020/01/20 16:53:41.160 -0500",
"request": "https://myserver/fhir-server/api/v4/$export?_type=Patient",
"requiresAccessToken": false,
"output" : [
{ "type" : "AllergyIntolerance",
"url": "https://s3.us-south.cloud-object-storage.appdomain.cloud/fhir-bulkimexport-connectathon/6SfXzbGvYl1nTjGbf5qeqJDFNjyljiGdKxXEJb4yJn8=/AllergyIntolerance_1.ndjson",
"count": 20},
{ "type" : "AllergyIntolerance",

For the Import Operation, the polled status includes an indication of $import and the location of the OperationOutcome NDJSON files and the corresponding failure and success counts.

For S3 exports, the bulk data feature may use presigned urls. To enable presigned urls, the authentication type must be hmac and fhirServer/bulkdata/storageProviders/(source)/presigned must be true. The urls become:

https://s3.appdomain.cloud/fhir-example/Patient_1.ndjson?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=fcEXbf9cc1ac49e99eEX77%2F20210228%2Fus%2Fs3%2Faws4_request&X-Amz-Date=20210EXT160538Z&X-Amz-Expires=86400&X-Amz-SignedHeaders=host&X-Amz-Signature=5ecfc207546b9737fd38d4f0EXEX1c58f4f82976338a44c

The presigned URL is valid for 86400 seconds (1 day).

To cancel a running job (or delete a completed job), issue an HTTP DELETE request to the polling URL.

  • Invoking DELETE on a running job will return HTTP 202 (Accepted) and stop the job
  • Invoking DELETE on a completed job will return HTTP 204 (Deleted) and delete the job
  • Invoking DELETE on a deleted job will return a 404 (Not Found)

Prior to version 4.8.1, the exported ndjson file is configured with public access automatically and with 2 hours expiration time using fhirServer/bulkdata/storageProviders/(source)/exportPublic. The exported content is best made available with presigned urls with the hmac authentication type.

In 4.8.1, the randomly generated path is used to uniquely identify the exported files in a single folder.

JavaBatch feature must be enabled in server.xml as following on the Liberty server:

<featureManager>
...
<feature>batchManagement-1.0</feature>
...
</featureManager>

The JavaBatch user is configured in bulkdata.xml and the fhir-server-config.json:

<authorization-roles id="com.ibm.ws.batch">
<security-role name="batchAdmin">
<user name="fhiradmin"/>
</security-role>
<security-role name="batchSubmitter">
<user name="fhiruser"/>
</security-role>
<security-role name="batchMonitor">
<user name="fhiradmin"/>

Note: The batch-user referenced in the fhir-server-config.json must have a role of at least batchSubmitter.

By default, in-memory Derby database is used for persistence of the JavaBatch Jobs as configured in fhir-server/configDropins/defaults/bulkdata.xml. This database is destroyed on the restart of the LinuxForHealth FHIR Server, and does not support load balancing.

If one wants to support Postgres with a user-name and password , one should copy fhir-server/configDropins/disabled/postgres/bulkdata.xml to fhir-server/configDropins/defaults/bulkdata.xml replacing the existing bulkdata.xml. One can configure the Datasource by setting the following environment variables:

VariableDefaultDescription
BATCH_DB_HOSTNAMEblankThe hostname of the postgres instance
BATCH_DB_NAMEFHIRDBThe database name
BATCH_DB_SCHEMAFHIR_JBATCHThe Schema Name configured to support the Java Batch framework
BATCH_DB_PORT5432The port configured to support the database
BATCH_DB_USERfhirserverThe user for the postgres database
BATCH_DB_PASSWORDblankThe password for the postgres database
BATCH_DB_SSLtrueThe ssl connection is either true or false
BATCH_DB_SSL_CERT_PATHfalseThe ssl connection is either true or false

Note: If you use a PostgreSQL database as the LinuxForHealth FHIR Server data store or the JavaBatch job repository, please enable max_prepared_transactions in postgresql.conf, otherwise the import/export JavaBatch jobs fail.

For more information about Liberty JavaBatch configuration, please refer to IBM WebSphere Liberty Java Batch White paper.

If you are running in a Kubernetes deployment, be sure to set the environment variable MY_POD_NAME to metadata.name as shown in deployment.yaml. This setting allows the stopping and deleting of jobs on all the hosts in the deployment.

4.10.1 Path and Virtual Host Bucket Access

For BulkData storage types of ibm-cos and aws-s3, the LinuxForHealth FHIR Server supports two styles of accessing the s3 bucket - virtual host and path. In the LinuxForHealth FHIR Server, path is the default access. Link

With path style access, the objects in a bucket are accessed using the pattern - https://s3.region.host-name.com/bucket-name/object-key. To configure path style access, one needs to configure the fhir-server-config.json.

There are three critical elements in the configuration to configure path style:

ConfigurationDetails
endpointInternalthe direct S3 API provider for the S3 API
endpointExternalthe endpoint url used to generate the downloadUrl used in S3 Export
accessType“path”, the default access type

Example of path based access:

"bulkdata": {
...
"storageProviders": {
"default" : {
"type": "aws-s3",
"bucketName": "bucket-name",
"location": "us",
"endpointInternal": "https://s3.region.host-name.com",
"endpointExternal": "https://s3.region.host-name.com",

With virtual host style access, the objects in a bucket are accessed using the pattern - https://bucket-name.s3.region.host-name.com/object-key. To configure virtual host style access, one needs to configure the API.

There are three critical elements in the configuration to configure virtual host style:

ConfigurationDetails
endpointInternalthe direct API provider for the S3 API, and not the virtual host, the underlying S3 libraries generate the virtual host url
endpointExternalthe Virtual Host endpoint url used to generate the downloadUrl generated after an Export
accessType“host”

Note, while the endpointInternal is specified with the S3 region endpoint, the calls to the API will use the virtual host directly.

Example of host based access:

"bulkdata": {
...
"storageProviders": {
"default" : {
"type": "aws-s3",
"bucketName": "bucket-name",
"location": "us",
"endpointInternal": "https://s3.region.host-name.com",
"endpointExternal": "https://bucket-name.s3.region.host-name.com",

4.10.2 S3 Import File with matching segments

When Importing from an S3 Bucket, the LinuxForHealth FHIR Server identifies the matching file segments. The parameter.input.url is used to query the S3 API to find the matching files. For instance, the following import of Patient.ndjson matches Patient.ndjson_seg0 and Patient.ndjson_seg1 which are imported to the LinuxForHealth FHIR Server.

This feature is useful for imports which follow a prefix pattern:

{
"resourceType": "Parameters",
"id": "30321130-5032-49fb-be54-9b8b82b2445a",
"parameter": [
{
"name": "inputFormat",
"valueString": "application/fhir+ndjson"
},
{

4.10.3 Integration Testing

There are tests in the fhir-server-test module for system, patient and group export. These tests rely on fhir-server-config files that currently exist under fhir-server-webapp/src/test/liberty.

4.10.5 Job Logs

Because the bulk import and export operations are built on Liberty’s java batch implementation, users may need to check the Liberty batch job logs for detailed step information / troubleshooting.

In a standard installation, these logs will be at wlp/usr/servers/fhir-server/logs/joblogs. In the ibmcom/ibm-fhir-server docker image, these logs will be at /logs/joblogs.

Note, if you are using the default Apache Derby, the logs are overwritten upon restart of the server. You should use PostgreSQL for production purposes.

4.10.6 Known Limitations

The LinuxForHealth FHIR Server’s fhir-bulkdata-webapp does not support persistence interceptors. Therefor, $import requests will not lead to beforeCreate/beforeUpdate or afterCreate/afterUpdate method calls and $export requests will not lead to beforeRead/beforeSearch or afterRead/afterSearch method calls. Because the LinuxForHealth FHIR Server’s notifications feature is implemented as a persistence interceptor, bulk operations will not result in any notification events.

4.11 Audit logging service

The Audit logging service pushes FHIR server audit events for FHIR operations in Cloud Auditing Data Federation (CADF) standard format to a Kafka backend, such as IBM Cloud Event Streams service.

There is early support for the FHIR Standard: AuditEvent format.

4.11.1 CADF audit log entry

Each FHIR interaction triggers a CADF audit log entry to be logged. The mapping of FHIR interaction to CADF action is as follows:

FHIR InteractionCADF Action
history,metadata,read,search,validate,version readread
createcreate
updateupdate
deletedelete
bundle,custom operation,patchunknown

The following table describes the JSON fields of the CADF audit log entries logged by the FHIR server:

CADF Audit Log Entry FieldDescription
actionAction that created the audit event. Possible values are “read”, “update”, “create”, “delete”, and “unknown”.
eventTimeAudit event creation timestamp.
eventTypeAudit event type. Value is always “activity”.
idGlobally unique identifier for the audit event.
outcomeAction outcome. Possible values are “success”, “failure”, “unknown”, and “pending”.
typeURITypeURI property of the CADF event entity. Value is always ”http://schemas.dmtf.org/cloud/audit/1.0/event”.
attachmentsNote: Contains FHIR server-specific audit event data.
attachments/contentTypeFHIR server-specific audit event data content type. Value is always “application/json”.
attachments/contentNote: Contents of this field (with its subfields) is encoded as Base64 with a 4-byte header.
attachments/content/request_unique_idGlobally unique identifier for the FHIR server request.
attachments/content/actionFHIR action type. Possible values are “C” (create), “U” (update), “R” (read), “D” (delete), “P” (patch), and “O” (custom operation).
attachments/content/operation_nameFHIR custom operation name.
attachments/content/start_timeFHIR request start time.
attachments/content/end_timeFHIR request end time.
attachments/content/api_parameters/requestFHIR request URL.
attachments/content/api_parameters/request_statusFHIR request HTTP status (e.g. 200).
attachments/content/data/resource_typeResource type of FHIR resource that was created, updated, or deleted.
attachments/content/data/idResource ID of FHIR resource that was created, updated, or deleted.
attachments/content/data/versionUpdated version of FHIR resource that was created, updated, or deleted.
attachments/content/batch/resources_readFHIR resource count retrieved on a search request.
attachments/content/event_typeFHIR event type. Possible values are “fhir-create”, “fhir-update”, “fhir-patch”, “fhir-delete”, “fhir-read”, “fhir-version-read”, “fhir-history”, “fhir-search”, “fhir-bundle”, “fhir-validate”, “fhir-metadata”, and “fhir-operation”.
attachments/content/descriptionFHIR event type description. Possible values are “FHIR Create request”, “FHIR Update request”, “FHIR Patch request”, “FHIR Delete request”, “FHIR Read request”, “FHIR VersionRead request”, “FHIR History request”, “FHIR Search request”, “FHIR Bundle request”, “FHIR Validate request”, “FHIR Metadata request”, and “FHIR Operation request”.
attachments/content/client_cert_cnValue is determined by “IBM-App-cli-CN” HTTP header of the FHIR request.
attachments/content/client_cert_issuer_ouValue is determined by “IBM-App-iss-OU” HTTP header of the FHIR request.
attachments/content/locationIP address and hostname of the source of the FHIR request.
initiator/idValue is always “TENANT_ID@fhir-server”, where TENANT_ID is replaced with the tenant ID.
initiator/typeURIValue is always “compute/machine”.
initiator/hostIP address of FHIR server localhost.
initiator/credential/tokenValue is always “user-AUTH_USER”, where AUTH_USER is replaced with the name of the authenticated user.
initiator/geolocation/cityValue determined by “fhirServer/audit/serviceProperties/geoCity” configuration property.
initiator/geolocation/stateValue determined by “fhirServer/audit/serviceProperties/geoState” configuration property.
initiator/geolocation/regionValue determined by “fhirServer/audit/serviceProperties/geoCounty” configuration property.
observer/idValue is always “fhir-server”.
observer/typeURIValue is always “compute/node”.
observer/nameValue is always “Fhir Audit”.
observer/geolocation/cityValue is determined by “fhirServer/audit/serviceProperties/geoCity” configuration property.
observer/geolocation/stateValue is determined by “fhirServer/audit/serviceProperties/geoState” configuration property.
observer/geolocation/regionValue is determined by “fhirServer/audit/serviceProperties/geoCounty” configuration property.
target/idValue is the Logical ID from the resource
target/typeUriValue is always “compute/node”.
target/addresses/urlValue determined by the HttpServletRequest for the server. The value does not use the X-FHIR-FORWARDED-URL http header
target/geolocation/cityValue determined by “fhirServer/audit/serviceProperties/geoCity” configuration property.
target/geolocation/stateValue determined by “fhirServer/audit/serviceProperties/geoState” configuration property.
target/geolocation/regionValue determined by “fhirServer/audit/serviceProperties/geoCounty” configuration property.

Note for Batch/Transactions, attachments/content includes counts of the number of C-R-U-D-E actions.

4.11.2 Enable audit logging service

Please refer to the property names that start with fhirServer/audit/ in 5.1 Configuration properties reference for how to enable and configure the CADF audit logging service.

4.11.3 Configuration of audit logging service

There are two types of configuration for the Audit Logging Service. The first type is using the environment variable, and the second is the configuration driven from the fhir-server-config.json.

For example, the following uses the ‘config’ in order to config the Kafka publisher as part of the audit logging service.

"audit": {
"serviceClassName" : "org.linuxforhealth.fhir.audit.impl.KafkaService",
"serviceProperties" : {
"load": "config",
}

Or, you could load from an environment, note, this is the default behavior.

"audit": {
"serviceClassName" : "org.linuxforhealth.fhir.audit.impl.KafkaService",
"serviceProperties" : {
"load": "environment",
}

4.11.3.1 Environment Variable Configuration of audit logging service

The audit logging service gets the event streams service credential from environment variable EVENT_STREAMS_AUDIT_BINDING with values like this:

{
"api_key": "xxxxxxxxxxxxxxxx_xxxxx_xxxxxxxxxxxxxxxxxxx",
"apikey": "xxxxxxxxxxxxxxxx_xxxxx_xxxxxxxxxxxxxxxxxxx",
"kafka_brokers_sasl": [
"broker-1-0server:9093",
"broker-2-0server:9093",
"broker-5-0server:9093",
"broker-4-0server:9093",

If you are using the IBM EventStreams on IBM Cloud, the service credential can be generated automatically when you run:

ibmcloud ks cluster-service-bind --cluster <cluster_name_or_ID> --namespace <namespace> --service <event_streams_service_instance_name> …

to bind your event streams service instance to your Kubernetes cluster.

And then in the YAML file for your Kubernetes deployment, specify the environment variable EVENT_STREAMS_AUDIT_BINDING that references the binding key of the generated secret(binding-<event_streams_service_instance_name>) as following:

- name: EVENT_STREAMS_AUDIT_BINDING
valueFrom:
secretKeyRef:
key: binding
name: binding-<event_streams_service_instance_name>

Please refer to https://cloud.ibm.com/docs/containers?topic=containers-service-binding for detailed instructions if needed.

4.11.3.2 fhir-server-config.json Configuration of audit logging service

"audit": {
"serviceClassName" : "org.linuxforhealth.fhir.audit.impl.KafkaService",
"serviceProperties" : {
"load": "config",
"mapper": "cadf",
"auditTopic": "FHIR_AUDIT",
"geoCity": "Dallas",
"geoState": "TX",
"geoCounty": "US",

The service can map to the CADF format or the FHIR AuditEvent resource format by declaring a mapper type - ‘cadf’ or ‘auditevent’.

  • CADF Example
{
"action": "create",
"eventTime": "2020-12-10 16:49:22.307",
"eventType": "activity",
"id": "c62ee8f8-be77-49d0-aad0-c0bf52a05fdf",
"outcome": "success",
"typeURI": "http://schemas.dmtf.org/cloud/audit/1.0/event",
"tags": [
],
  • AuditEvent Example
{
"resourceType": "AuditEvent",
"type": {
"system": "http://terminology.hl7.org/CodeSystem/audit-event-type",
"code": "rest",
"display": "Restful Operation"
},
"subtype": [
{

4.11.4 Query CADF events in COS

Watson Studio stream flow can be created to push those FHIR Audit CADF events from the Event Streams service to a COS bucket (e.g. fhir-audit-dev) in CSV format. Another option is to configure Event Streams (Kafka) S3 connect to push those CADF events to a COS bucket (e.g. fhir-audit-dev) but in raw CADF json format.

A service instance of the IBM Cloud SQL Query service can be created to allow you to query those CADF audit events in COS with SQL queries. Before running an SQL query, it’s recommended to first create a COS bucket to store your query results, otherwise the query results will be stored in a bucket which is automatically created by the SQL query service.

Sample queries for CSV records expanded from the JSON CADF events:

select * from cos://us-south/fhir-audit-dev where EVENTTIME BETWEEN "2019-06-07" and "2019-06-08" and action="unknown" into cos://us-south/fhir-audit-dev-res stored as csv
select action, count(*) from cos://us-south/fhir-audit-dev where EVENTTIME BETWEEN "2019-06-05" and "2019-06-06" group by action into cos://us-south/fhir-audit-dev-res stored as csv
select * from cos://us-south/fhir-audit-dev where EVENTTIME BETWEEN "2019-06-05" and "2019-06-06" and action="create" and initiator_id="default@fhir-server" into cos://us-south/fhir-audit-dev-res stored as csv
select * from cos://us-south/fhir-audit-dev where EVENTTIME BETWEEN "2019-06-05" and "2019-06-06" and ATTACHMENTS_CONTENT LIKE '%fhir-read%' into cos://us-south/fhir-audit-dev-res stored as csv

Sample queries for the raw JSON CADF events:

select * from cos://us-south/fhir-audit-dev0 stored as json where EVENTTIME BETWEEN "2019-06-01" and "2019-06-08" and action="unknown" into cos://us-south/fhir-audit-dev0-res stored as json
select action, count(*) from cos://us-south/fhir-audit-dev0 stored as json where EVENTTIME BETWEEN "2019-06-01" and "2019-06-06" group by action into cos://us-south/fhir-audit-dev0-res stored as csv
select * from cos://us-south/fhir-audit-dev0 stored as json where EVENTTIME BETWEEN "2019-06-01" and "2019-06-06" and action="create" and initiator.id="default@fhir-server" into cos://us-south/fhir-audit-dev-res stored as json
select * from cos://us-south/fhir-audit-dev0 stored as json where EVENTTIME BETWEEN "2019-06-01" and "2019-06-06" and ATTACHMENTS[0].CONTENT LIKE '%fhir-read%' into cos://us-south/fhir-audit-dev-res stored as json

4.12 FHIR REST API

By default, the LinuxForHealth FHIR Server allows the following RESTful interactions associated with the FHIR REST API: create, read, vread, history, search, update, patch, delete. However, it is possible to configure which of these interactions are allowed on a per resource basis through a set of interaction rules specified via the fhirServer/resources/<resourceType>/interactions property in fhir-server-config.json. The following snippet shows the general form for specifying interaction rules:

"resources": {
"open": true,
"Condition": {
"interactions": ["create", "read", "vread", "history", "search", "update", "patch", "delete"]
},
"Observation": {
"interactions": ["create", "read", "vread", "history", "delete"]
},
"Patient": {

The fhirServer/resources/<resourceType>/interactions property is a JSON array of strings that represent the RESTful interactions allowed for the given resource type. If an interaction is not in the list of strings specified for a resource type, that interaction will not be allowed for that resource type. In the example above, the following interactions are allowed for the Observation resource type: [create, read, vread, history, delete]. This means a user will not be able to search for Observation resources because the search interaction is not specified in the list of allowed interactions.

Omitting the fhirServer/resources/<resourceType>/interactions property is equivalent to allowing all interactions for a given resource type. An empty array, [], can be used to indicate that no interactions are allowed. Additionally, to define the set of interactions allowed for resource types which are not specifically configured in the fhirServer/resources property group, or for resource types which are configured, but which do not specify the fhirServer/resources/<resourceType>/interactions property, the base type of Resource may be specified:

"resources": {
"open": true,
"Condition": {
"interactions": ["create", "read", "vread", "history", "search", "update", "delete"]
},
"Observation": {
"interactions": ["create", "read", "vread", "history", "delete"]
},
"Patient": {

In the example above, for any resource type which is not specifically configured, such as Encounter, or for any resource type which is configured but does not specify the fhirServer/resources/<resourceType>/interactions property, such as Procedure, all of the interactions listed for the Resource resource type will be allowed.

One final consideration when configuring interactions is the fhirServer/resources/open property. If this property is specified and its value is set to false, then no interactions will be allowed for resource types which are not specifically listed in the fhirServer/resources property group. Assume the following configuration:

"resources": {
"open": false,
"Condition": {
"interactions": ["create", "read", "vread", "history", "search", "update", "delete"]
},
"Observation": {
"interactions": ["create", "read", "vread", "history", "delete"]
},
"Patient": {

In this case, since the fhirServer/resources/open property is set to false, only the resource types listed (Condition, Observation, Patient) are allowed to be interacted with via the FHIR REST API. For example, a create request of a Procedure resource will fail since that resource type is not specified.

Whole-system search and whole-system history are special cases. Since no resource type is specified on a whole-system request, validation will be done against the Resource resource type. In the above configuration example, a whole-system search request such as GET [base]?_lastUpdated=gt2020-01-01 will fail because the Resource resource type is not specified. If the configuration were to have the fhirServer/resources/open property set to true, or if the Resource resource type were specified in the fhirServer/resources property group, then the whole-system search request would be allowed, assuming the search interaction was valid for the Resource resource type.

In addition to interaction configuration, the fhirServer/resources property group also provides the ability to configure search parameter filtering and profile validation. See Search configuration and Resource validation respectively for details.

Unlike most other tenant-specific properties, the fhirServer/resources property group is processed as a single unit. In the event that fhirServer/resources exists in a tenant-specific config, but a particular sub-property is missing (e.g. fhirServer/resources/open), that sub-property will not inheret from the “default” tenant.

4.12.1 Using the LinuxForHealth FHIR Server behind a proxy

It is possible to run the LinuxForHealth FHIR Server behind a reverse proxy such as Kubernetes Ingress or an API Gateway.

Because the FHIR API relies on links and references between resources (both absolute and relative), operators must ensure that the LinuxForHealth FHIR Server is configured appropriately for the front-end URL being used by the FHIR clients.

This can be accomplished by configuring the fhirServer/core/originalRequestUriHeaderName property in the default fhir-server-config.json. When this parameter is configured, the LinuxForHealth FHIR Server will use the value of the corresponding header to set the “originalRequestUri” for the scope of the request.

For example, consider a FHIR Server that is listening at https://fhir:9443/fhir-server/api/v4 and is configured with an originalRequestUriHeaderName of X-FHIR-FORWARDED-URL. If this server is proxied by a server at https://example.com/fhir, then the proxy must set the X-FHIR-FORWARDED-URL header to the value of the front-end request URL (e.g. https://example.com/fhir/Patient/abc-123). In alternative deployments, the fhirServer/core/externalBaseUrl may be used in-lieu of the X-FHIR-FORWARDED-URL.

The originalRequestUriHeader is expected to contain the full path of the original request. Values with no scheme (e.g. https://) will be handled like relative URLs, but full URL values (including scheme, hostname, optional port, and path) are recommended. Query string values can be included in the header value but will be ignored by the server; the server will use the query string of the actual request to process the request.

4.13 Remote Index Service

To use the experimental remote index service feature, see the instructions documented in the fhir-remote-index project.

5 Appendix

5.1 Configuration properties reference

This section contains reference information about each of the configuration properties supported by the FHIR server.

5.1.1 Property descriptions

Property NameTypeDescription
fhirServer/core/defaultPrettyPrintbooleanA boolean flag which indicates whether “Pretty Printing” should be used by default. Applies to both XML and JSON.
fhirServer/core/tenantIdHeaderNamestringThe name of the request header that will be used to specify the tenant-id for each incoming FHIR REST API request. For headers with semicolon-delimited parts, setting a header name like <headerName>:<partName> will select the value from the part of header <headerName>’s value with a name of <partName> (e.g. setting X-Test:part1 would select someValue from the header X-Test: part1=someValue;part2=someOtherValue).
fhirServer/core/dataSourceIdHeaderNamestringThe name of the request header that will be used to specify the datastore-id for each incoming FHIR REST API request. For headers with semicolon-delimited parts, setting a header name like <headerName>:<partName> will select the value from the part of header <headerName>’s value with a name of <partName> (e.g. setting X-Test:part1 would select someValue from the header X-Test: part1=someValue;part2=someOtherValue).
fhirServer/core/originalRequestUriHeaderNamestringThe name of the request header that will be used to indicate the original, end-user-facing, request URI for a given request. This optional config parameter is provided for cases where the server is deployed behind a reverse proxy that overwrites the host and/or path portions of the original request.
fhirServer/core/defaultHandlingstringThe default handling preference of the server (strict or lenient) which determines how the server handles unrecognized search parameters and resource elements.
fhirServer/core/allowClientHandlingPrefbooleanIndicates whether the client is allowed to override the server default handling preference using the Prefer:handling header value part.
fhirServer/core/checkReferenceTypesbooleanIndicates whether reference type checking is performed by the server during parsing / deserialization.
fhirServer/core/checkControlCharactersbooleanIndicates whether Strings and Codes are checked for invalid control characters (ASCII and UTF-8).
fhirServer/core/serverRegistryResourceProviderEnabledbooleanIndicates whether the server registry resource provider should be used by the FHIR registry component to access definitional resources through the persistence layer.
fhirServer/core/serverResolveFunctionEnabledbooleanIndicates whether the server resolve function should be used by the FHIRPath evaluator to resolve references through the persistence layer.
fhirServer/core/conditionalDeleteMaxNumberintegerThe maximum number of matches supported in conditional delete.
fhirServer/core/capabilityStatementCacheTimeoutintegerThe number of minutes that a tenant’s CapabilityStatement is cached for the metadata endpoint.
fhirServer/core/extendedCodeableConceptValidationbooleanA boolean flag which indicates whether extended validation is performed by the server during object construction for code, Coding, CodeableConcept, Quantity, Uri, and String elements which have required bindings to value sets.
fhirServer/core/disabledOperationsstringA comma-separated list of operations which are not allowed to run on the LinuxForHealth FHIR Server, for example, validate,import. Note, do not include the dollar sign $
fhirServer/core/defaultPageSizeintegerSets the page size for search and history request results when no _count parameter is specified.
fhirServer/core/maxPageSizeintegerSets the maximum page size for search and history request results. If a user-specified _count parameter value exceeds the maximum page size, then a warning is logged and the maximum page size will be used.
fhirServer/core/maxPageIncludeCountintegerSets the maximum number of ‘include’ resources allowed per page for search and history request results. If the number of ‘include’ resources returned for a page of results from a search or history request will exceed the maximum number of ‘include’ resources allowed per page, then an error will be returned in the request results.
fhirServer/core/ifNoneMatchReturnsNotModifiedbooleanWhen If-None-Match: * is specified for PUT requests, overrides the standard return status “412 Precondition Failed” to be “304 Not Modified”. Useful in transaction bundles for clients not wanting the bundle to fail when a conflict is found.
fhirServer/core/capabilitiesUrlstringThe URL that is embedded in the default Capabilities statement
fhirServer/core/externalBaseUrlstringThe base URL that is embedded in the Search bundle response, as of version 4.9.0. Note that the base URL must not include a path segment that matches any FHIR resource type name (case-sensitive). For example, ”https://example.com” or ”https://example.com/my/patient/api” are fine, but ”https://example.com/my/Patient/api” is not.
fhirServer/core/defaultFhirVersionstringThe implicit value to use for the MIME-type fhirVersion parameter on incoming Accept and Content-Type headers when the client has not passed an explicit value.
fhirServer/core/useImplicitTypeScopingForWholeSystemInteractionsbooleanWhether to apply implicit resource type scoping for whole-system search and whole-system history interactions where no _type values were passed. Only set to false if you are certain that there are no instances of unsupported resource types in the database.
fhirServer/validation/failFastbooleanIndicates whether validation should fail fast on create and update interactions
fhirServer/term/capabilitiesUrlstringThe URL that is embedded in the Terminology Capabilities statement using mode=terminology
fhirServer/term/disableCachingbooleanIndicates whether caching is disabled for the FHIR terminology module, this includes caching in CodeSystemSupport, ValueSetSupport, GraphTermServiceProvider, and RemoteTermServiceProvider
fhirServer/term/graphTermServiceProvidersarray of objectsThe graphTermServiceProviders element is an array of objects
fhirServer/term/graphTermServiceProviders/enabledbooleanIndicates whether the graph term service provider should be used by the FHIR term service to access code system content
fhirServer/term/graphTermServiceProviders/timeLimitintegerGraph traversal time limit (in milliseconds)
fhirServer/term/graphTermServiceProviders/configurationobject (name/value pairs)A JSON object that contains the name/value pairs used to configure the graph database behind the graph term service provider see: https://docs.janusgraph.org/basics/configuration-reference/
fhirServer/term/remoteTermServiceProvidersarray of objectsThe remoteTermServiceProviders element is an array of objects
fhirServer/term/remoteTermServiceProviders/enabledbooleanIndicates whether this remote term service provider should be used by the FHIR term service to access code system content
fhirServer/term/remoteTermServiceProviders/basestringThe base URL for this remote term service provider
fhirServer/term/remoteTermServiceProviders/trustStore/locationstringThe trust store location for this remote term service provider
fhirServer/term/remoteTermServiceProviders/trustStore/passwordstringThe trust store password for this remote term service provider
fhirServer/term/remoteTermServiceProviders/trustStore/typestringThe trust store type (e.g. pkcs12) for this remote term service provider
fhirServer/term/remoteTermServiceProviders/hostnameVerificationEnabledbooleanIndicates whether hostname verification should be performed when using SSL transport
fhirServer/term/remoteTermServiceProviders/basicAuth/usernamestringThe basic authentication username for this remote term service provider
fhirServer/term/remoteTermServiceProviders/basicAuth/passwordstringThe basic authentication password for this remote term service provider
fhirServer/term/remoteTermServiceProviders/headersarray of objectsThe headers element is an array of objects
fhirServer/term/remoteTermServiceProviders/headers/namestringThe HTTP header name that will be added to requests by this remote term service provider
fhirServer/term/remoteTermServiceProviders/headers/valuestringThe HTTP header value that will be added to requests by this remote term service provider
fhirServer/term/remoteTermServiceProviders/httpTimeoutintegerThe HTTP read timeout for this remote term service provider (in milliseconds)
fhirServer/term/remoteTermServiceProviders/supportsarray of objectsThe supports element is an array of objects
fhirServer/term/remoteTermServiceProviders/supports/systemstringThe system URI supported by this remote term service provider
fhirServer/term/remoteTermServiceProviders/supports/versionstringThe system version supported by this remote term service provider
fhirServer/resources/openbooleanWhether resources that are not explicitly listed in the configuration should be supported by the FHIR Server REST layer. When open is set to false, only the resources listed in fhir-server-config.json are supported.
fhirServer/resources/Resource/interactionsstring listA list of strings that represent the RESTful interactions (create, read, vread, update, patch, delete, history, and/or search) supported for resource types. Omitting this property is equivalent to supporting all FHIR interactions for the supported resources. An empty list, [], can be used to indicate that no REST methods are supported. This property can be overridden for specific resource types via the fhirServer/resources/<resourceType>/interactions property.
fhirServer/resources/Resource/searchParametersobjectThe set of search parameters to support for all supported resource types. Omitting this property is equivalent to supporting all search parameters in the server’s registry that apply to resource type “Resource” (all resources). An empty object, {}, can be used to indicate that no global search parameters are supported.
fhirServer/resources/Resource/searchParameters/<code>stringThe URL of the search parameter definition to use for the search parameter <code>. Individual resource types may override this value via fhirServer/resources/<resourceType>/searchParameters/<code>
fhirServer/resources/Resource/searchIncludesstring listA comma-separated list of _include values supported for all resource types. Individual resource types may override this value via fhirServer/resources/<resourceType>/searchIncludes. Omitting this property is equivalent to supporting all _include values for the supported resources. An empty list, [], can be used to indicate that no _include values are supported.
fhirServer/resources/Resource/searchRevIncludesstring listA comma-separated list of _revinclude values supported for all resource types. Individual resource types may override this value via fhirServer/resources/<resourceType>/searchRevIncludes. Omitting this property is equivalent to supporting all _revinclude values for the supported resources. An empty list, [], can be used to indicate that no _revinclude values are supported.
fhirServer/resources/Resource/searchParameterCombinationsstring listA comma-separated list of search parameter combinations supported for all resource types. Each search parameter combination is a string, where a plus sign, +, separates the search parameters that can be used in combination. To indicate that searching without any search parameters is allowed, an empty string must be included in the list. Including an asterisk, *, in the list indicates support of any search parameter combination. Individual resource types may override this value via fhirServer/resources/<resourceType>/searchParameterCombinations. Omitting this property is equivalent to supporting any search parameter combination.
fhirServer/resources/Resource/profiles/atLeastOnestring listA comma-separated list of profiles, at least one of which must be specified in a resource’s meta.profile element and successfully validated against in order for a resource to be persisted to the FHIR server. Individual resource types may override this value via fhirServer/resources/<resourceType>/profiles/atLeastOne. Omitting this property or specifying an empty list is equivalent to not requiring any profile assertions for a resource.
fhirServer/resources/Resource/profiles/notAllowedstring listA comma-separated list of profiles that are not allowed to be specified in a resource’s meta.profile element, and thus cannot be validated against in order for a resource to be persisted to the FHIR server. Individual resource types may override this value via fhirServer/resources/<resourceType>/profiles/notAllowed. Omitting this property or specifying an empty list is equivalent to allowing any profile assertions for a resource.
fhirServer/resources/Resource/profiles/allowUnknownbooleanIndicates if profiles are allowed to be specified in a resource’s meta.profile element that are not loaded in the FHIR server. If set to false, specifying a profile that is not loaded in the FHIR server results in an error and a resource validation failure. If set to true, a warning will be issued and the profile will be ignored. The default value is true. Individual resource types may override this value via fhirServer/resources/<resourceType>/profiles/allowUnknown.
fhirServer/resources/Resource/profiles/defaultVersionsobjectA set of profiles for which default profile versions are specified. If a profile in this set is asserted for a resource, and the asserted profile URL does not include a version, the version specified for the profile in this set will be used during resource validation. In cases where asserted profiles do not include a version, and are not in this set, the FHIR server will determine the default version of the profile to be used during resource validation. Individual resource types may override this set of profiles via fhirServer/resources/<resourceType>/profiles/defaultVersions.
fhirServer/resources/Resource/profiles/defaultVersions/<profile>stringThe version of the profile definition to use for the profile <profile> during resource validation when this profile is asserted.
fhirServer/resources/<resourceType>/interactionsstring listA list of strings that represent the RESTful interactions (create, read, vread, update, patch, delete, history, and/or search) to support for this resource type. For resources without the property, the value of fhirServer/resources/Resource/interactions is used.
fhirServer/resources/<resourceType>/searchParametersobjectThe set of search parameters to support for this resource type. Global search parameters defined on the Resource resource can be overridden on a per-resourceType basis.
fhirServer/resources/<resourceType>/searchParameters/<code>stringThe URL of the search parameter definition to use for the search parameter <code> on resources of type <resourceType>.
fhirServer/resources/<resourceType>/searchIncludesstring listA comma-separated list of _include values supported for this resource type. An empty list, [], can be used to indicate that no _include values are supported. For resources without the property, the value of fhirServer/resources/Resource/searchIncludes is used.
fhirServer/resources/<resourceType>/searchRevIncludesstring listA comma-separated list of _revinclude values supported for this resource type. An empty list, [], can be used to indicate that no _revinclude values are supported. For resources without the property, the value of fhirServer/resources/Resource/searchRevIncludes is used.
fhirServer/resources/<resourceType>/searchParameterCombinationsstring listA comma-separated list of search parameter combinations supported for this resource type. Each search parameter combination is a string, where a plus sign, +, separates the search parameters that can be used in combination. To indicate that searching without any search parameters is allowed, an empty string must be included in the list. Including an asterisk, *, in the list indicates support of any search parameter combination. For resources without the property, the value of fhirServer/resources/Resource/searchParameterCombinations is used.
fhirServer/resources/<resourceType>/profiles/atLeastOnestring listA comma-separated list of profiles, at least one of which must be specified in a resource’s meta.profile element and be successfully validated against in order for a resource of this type to be persisted to the FHIR server. If this property is not specified, the value of fhirServer/resources/Resource/profiles/atLeastOne will be used. If an empty list is specified, it is equivalent to not requiring any profile assertions for this resource type.
fhirServer/resources/<resourceType>/profiles/notAllowedstring listA comma-separated list of profiles that are not allowed to be specified in a resource’s meta.profile element, and thus cannot be validated against in order for a resource to be persisted to the FHIR server. If this property is not specified, the value of fhirServer/resources/Resource/profiles/notAllowed will be used. If an empty list is specified, it is equivalent to allowing any profile assertions for this resource type.
fhirServer/resources/<resourceType>/profiles/allowUnknownbooleanIndicates if profiles are allowed to be specified in a resource’s meta.profile element that are not loaded in the FHIR server. If set to false, specifying a profile that is not loaded in the FHIR server results in an error and a resource validation failure. If set to true, a warning will be issued and the profile will be ignored. If this property is not specified, the value of fhirServer/resources/Resource/profiles/allowUnknown will be used.
fhirServer/resources/<resourceType>/profiles/defaultVersionsobjectA set of profiles for which default profile versions are specified for this resource type. If a profile in this set is asserted for a resource, and the asserted profile URL does not include a version, the version specified for the profile in this set will be used during resource validation. In cases where asserted profiles do not include a version, and are not in this set, the FHIR server will determine the default version of the profile to be used during resource validation. If this property is not specified, the value of fhirServer/resources/Resource/profiles/defaultVersions will be used.
fhirServer/resources/<resourceType>/profiles/defaultVersions/<profile>stringThe version of the profile definition to use for the profile <profile> during resource validation when this profile is asserted for this resource type.
fhirServer/notifications/common/includeResourceTypesstring listA comma-separated list of resource types for which notification event messages should be published.
fhirServer/notifications/common/maxNotificationSizeBytesintegerThe maximum size in bytes of the notification that should be sent
fhirServer/notifications/common/maxNotificationSizeBehaviorstringThe behavior of the notification framework when a notification is over the maxNotificationSizeBytes. Valid values are subset and omit
fhirServer/notifications/websocket/enabledbooleanA boolean flag which indicates whether or not websocket notifications are enabled.
fhirServer/notifications/kafka/enabledbooleanA boolean flag which indicates whether or not kafka notifications are enabled.
fhirServer/notifications/kafka/syncbooleanA boolean flag which indicates whether or not the FHIRNotificationEvent is sent in a synchronous mode
fhirServer/notifications/kafka/topicNamestringThe name of the topic to which kafka notification event messages should be published.
fhirServer/notifications/kafka/connectionPropertiesproperty listA group of connection properties used to configure the KafkaProducer. These properties are used as-is when instantiating the KafkaProducer used by the FHIR server for publishing notification event messages.
fhirServer/notifications/nats/enabledbooleanA boolean flag which indicates whether or not NATS notifications are enabled.
fhirServer/notifications/nats/clusterstringThe name of the NATS streaming cluster to which to connect.
fhirServer/notifications/nats/channelstringThe name of the NATS channel on which NATS notification event messages are to be published.
fhirServer/notifications/nats/clientIdstringThe name to use for the connections to the NATS streaming cluster.
fhirServer/notifications/nats/serversstringThe URL of one or more NATS servers in the NATS streaming cluster.
fhirServer/notifications/nats/useTLSbooleanA boolean flag which indicates whether or not to use TLS for connections to the NATS streaming cluster.
fhirServer/notifications/nats/truststoreLocationstringThe file location of the truststore to use for TLS.
fhirServer/notifications/nats/truststorePasswordstringThe password for the truststore.
fhirServer/notifications/nats/keystoreLocationstringThe file location of the keystore to use for TLS.
fhirServer/notifications/nats/keystorePasswordstringThe password for the keystore.
fhirServer/persistence/payload/<datasourceId>/typestringazure.blob for Azure Blob offloading.
fhirServer/persistence/payload/<datasourceId>/connectionPropertiesmapConnection properties for Azure Blob
fhirServer/persistence/payload/<datasourceId>/connectionProperties/serviceVersionstringThe Azure Blob service version name (null for latest).
fhirServer/persistence/payload/<datasourceId>/connectionProperties/connectionStringstringThe Azure Blob service connection string.
fhirServer/persistence/payload/<datasourceId>/connectionProperties/containerNamestringThe name of the Azure Blob container created to store the payload offload data.
fhirServer/persistence/factoryClassnamestringThe name of the factory class to use for creating instances of the persistence layer implementation.
fhirServer/persistence/common/updateCreateEnabledbooleanA boolean flag which indicates whether or not the ‘update/create’ feature should be enabled in the selected persistence layer.
fhirServer/persistence/datasourcesmapA map containing datasource definitions. See Section 3.3.1 The JDBC persistence layer for more information.
fhirServer/persistence/datasources/<datasourceId>/typestringderby, postgresql or citus
fhirServer/persistence/datasources/<datasourceId>/jndiNamestringThe non-default jndiName for the datasource
fhirServer/persistence/datasources/<datasourceId>/currentSchemastringThe current schema for the datasource
fhirServer/persistence/datasources/<datasourceId>/searchOptimizerOptions/from_collapse_limitintFor PostgreSQL, sets the from_collapse_limit query optimizer parameter to improve search performance. If not set, the LinuxForHealth FHIR Server uses a value of 12. To use the database default (8), explicitly set this value to null.
fhirServer/persistence/datasources/<datasourceId>/searchOptimizerOptions/join_collapse_limitintFor PostgreSQL, sets the join_collapse_limit query optimizer parameter to improve search performance. If not set, the LinuxForHealth FHIR Server uses a value of 12. To use the database default (8), explicitly set this value to null.
fhirServer/security/corsbooleanUsed to convey to clients whether cors is supported or not; actual cors support is configured separately in the Liberty server.xml configuration
fhirServer/security/basic/enabledbooleanWhether or not the server is enabled for HTTP Basic authentication
fhirServer/security/certificates/enabledbooleanWhether or not the server is enabled for Certificate-based client authentication
fhirServer/security/oauth/enabledbooleanWhether or not the server is enabled for OAuth-based authentication/authorization
fhirServer/security/oauth/regUrlstringThe registration URL associated with the OAuth 2.0 authentication/authorization support.
fhirServer/security/oauth/authUrlstringThe authorization URL associated with the OAuth 2.0 authentication/authorization support.
fhirServer/security/oauth/tokenUrlstringThe token URL associated with the OAuth 2.0 authentication/authorization support.
fhirServer/security/oauth/manageUrlstringThe URL where an end-user can view which applications currently have access to data and can make adjustments to these access rights.
fhirServer/security/oauth/introspectUrlstringThe URL of the server’s introspection endpoint that can be used to validate a token.
fhirServer/security/oauth/revokeUrlstringThe URL to the server’s endpoint that can be used to revoke a token.
fhirServer/security/oauth/smart/enabledbooleanWhether or not the server is enabled for OAuth-based authentication/authorization
fhirServer/security/oauth/smart/scopesarrayThe list of SMART scopes to advertise in the `.well-known/smart-configuration endpoint
fhirServer/security/oauth/smart/capabilitiesarrayThe list of SMART capabilities to advertise in the `.well-known/smart-configuration endpoint
fhirServer/security/validateBinarySecurityContextbooleanWhether or not the securityContext validation is enabled for Binary resources
fhirServer/audit/serviceClassNamestringThe audit service to use. Currently, org.linuxforhealth.fhir.audit.impl.NopService to indicate the logger service is disabled, and org.linuxforhealth.fhir.audit.impl.KafkaService to indicate using Kafka as a destination.
fhirServer/audit/serviceProperties/auditTopicstringThe kafka topic to use for CADF audit logging service
fhirServer/audit/serviceProperties/geoCitystringThe Geo City configured for audit logging service.
fhirServer/audit/serviceProperties/geoStatestringThe Geo State configured for audit logging service.
fhirServer/audit/serviceProperties/geoCountystringThe Geo Country configured for audit logging service.
fhirServer/audit/serviceProperties/kafkaServersstringThe CSV list of Kafka brokers.
fhirServer/audit/serviceProperties/kafkaApiKeystringThe apikey for the JAAS configuration.
fhirServer/audit/serviceProperties/mapperstringThe AuditEventLog mapper that determines the output format - valid types are ‘cadf’ and ‘auditevent’. ‘auditevent’ refers to the FHIR Resource AuditEvent, and ‘cadf’ refers to the Cloud logging standard.
fhirServer/audit/serviceProperties/loadstringThe location that the configuration is loaded from ‘environment’ or ‘config’.
fhirServer/audit/serviceProperties/kafkaobjectA set of name value pairs used as part of the ‘config’ for publishing to the kafka service. These should only be Kafka properties.
fhirServer/audit/hostnamestringA string used to identify the Hostname, useful in containerized environments
fhirServer/audit/ipstringA string used to identify the IP address, useful to identify only one IP
fhirServer/search/useBoundingRadiusbooleanIf true then the bounding area is a radius, else the bounding area is a box.
fhirServer/search/enableLegacyWholeSystemSearchParamsbooleanTrue, searches specifying whole-system search parameters _profile, _tag, and _security run against legacy search index data, else those searches run against new search index data. This property can be set to true before a reindex operation is run, and after migrating to IBM FHIR Server version 4.9.0, to allow searches to work while the reindex operation is in progress. After the reindex has completed successfully, the property should be set to false or removed from the configuration.
fhirServer/bulkdata/enabledstringEnabling the BulkData operations
fhirServer/bulkdata/core/api/urlstringThe URL to access the FHIR server hosting the batch web application
fhirServer/bulkdata/core/api/userstringUser for submitting JavaBatch job
fhirServer/bulkdata/core/api/passwordstringPassword for above batch user
fhirServer/bulkdata/core/api/truststorestringTrust store for JavaBatch job submission
fhirServer/bulkdata/core/api/truststorePasswordstringPassword for above trust store
fhirServer/bulkdata/core/api/trustAllbooleanIndicates calls to the local API should skip hostname verification
fhirServer/bulkdata/core/cos/partUploadTriggerSizeMBnumberThe size, in megabytes, at which to write a “part” for multi-part uploads. The S3 API requires parts to be between 5 and 5000 MB and does not allow more than 10,000 parts per object.
fhirServer/bulkdata/core/cos/objectSizeThresholdMBnumberThe size, in megabytes, at which to finish writing a given object. Use 0 to indicate that all resources of a given type should be written to a single object, but be aware that S3 objects can have a maximum of 10,000 parts and a maximum size of 5,000,000 MB (5 TB).
fhirServer/bulkdata/core/cos/objectResourceCountThresholdnumberThe number of resources at which to finish writing a given object. The actual number of resources written to a single object may be slightly above this number, dependent on the configured page size. Use 0 to indicate that there is no limit to the number of resources to be written to a single object.
fhirServer/bulkdata/core/cos/requestTimeoutnumberThe request timeout in second for the COS client
fhirServer/bulkdata/core/cos/socketTimeoutnumberThe socket timeout in second for the COS client
fhirServer/bulkdata/core/cos/useServerTruststorebooleanIf the COS Client should use the LinuxForHealth FHIR Server’s TrustStore to access S3/IBMCOS service
fhirServer/bulkdata/core/cos/presignedExpirynumberThe time in seconds of the presigned download URL; must be using HMAC auth
fhirServer/bulkdata/core/file/writeTriggerSizeMBnumberThe size, in megabytes, at which to write the buffer to file.
fhirServer/bulkdata/core/file/sizeThresholdMBnumberThe size, in megabytes, at which to finish writing a given file. Use 0 to indicate that all resources of a given type should be written to a single file.
fhirServer/bulkdata/core/file/resourceCountThresholdnumberThe number of resources at which to finish writing a given file. The actual number of resources written to a single file may be slightly above this number, dependent on the configured page size. Use 0 to indicate that there is no limit to the number of resources to be written to a single file.
fhirServer/bulkdata/core/azure/objectSizeThresholdMBnumberThe size, in megabytes, at which to finish writing a given object.
fhirServer/bulkdata/core/azure/objectResourceCountThresholdnumberThe number of resources at which to finish writing a given object. The actual number of resources written to a single object may be slightly above this number, dependent on the configured page size.
fhirServer/bulkdata/core/batchIdEncodingKeystringEncoding key for JavaBatch job id
fhirServer/bulkdata/core/pageSizenumberThe search page size for patient/group export and the legacy export, the default value is 1000
fhirServer/bulkdata/core/maxPartitionsnumberThe maximum number of simultaneous partitions that are processed per Export and Import
fhirServer/bulkdata/core/maxInputsnumberThe number of inputs allowed for $import
fhirServer/bulkdata/core/iamEndpointstringOverride the system’s IAM endpoint
fhirServer/bulkdata/core/maxChunkReadTimestringMaximum time in milliseconds to read during a bulkdata export without type filters. The time should be three quarters of the transactionManager timeout (often the FHIR_TRANSACTION_MANAGER_TIMEOUT value). Note, this value is a string representation of a long value.
fhirServer/bulkdata/core/defaultExportProviderstringThe default storage provider used by Bulk Data Export
fhirServer/bulkdata/core/defaultImportProviderstringThe default storage provider used by Bulk Data Import
fhirServer/bulkdata/core/defaultOutcomeProviderstringThe default storage provider used to output Operation Outcomes (file, s3 only)
fhirServer/bulkdata/core/enableSkippableUpdatesbooleanEnables the skipping of identical resources
fhirServer/bulkdata/storageProviders/<source>/typestringThe type of storageProvider aws-s3, ibm-cos, file, https, azure-blob
fhirServer/bulkdata/storageProviders/<source>/bucketNamestringObject store bucket name
fhirServer/bulkdata/storageProviders/<source>/locationstringObject store location
fhirServer/bulkdata/storageProviders/<source>/endpointInternalstringObject store end point url used to read/write from COS
fhirServer/bulkdata/storageProviders/<source>/endpointExternalstringObject store end point url used in the constructed download URLs
fhirServer/bulkdata/storageProviders/<source>/fileBasestringThe absolute path of the output directory. It is recommended this path is not the mount point of a volume. For instance, if a volume is mounted to /output/bulkdata, use /output/bulkdata/data to ensure a failed mount does not result in writing to the root file system.
fhirServer/bulkdata/storageProviders/<source>/validBaseUrlslistThe list of supported urls which are approved for the fhir server to access
fhirServer/bulkdata/storageProviders/<source>/disableBaseUrlValidationbooleanDisables the URL checking feature, allowing all URLs to be imported
fhirServer/bulkdata/storageProviders/<source>/disableOperationOutcomesbooleanDisables the base url validation, allowing all URLs to be imported
fhirServer/bulkdata/storageProviders/<source>/duplicationCheckbooleanEnables duplication check on import
fhirServer/bulkdata/storageProviders/<source>/validateResourcesbooleanEnables the validation of imported resources
fhirServer/bulkdata/storageProviders/<source>/presignedbooleanWhen an hmac auth type is used, presigns the URLs of an export
fhirServer/bulkdata/storageProviders/<source>/createbooleanEnables the creation of buckets
fhirServer/bulkdata/storageProviders/<source>/serviceVersionstringAzure service version to support older instances of the service (for example V2020_12_06)
fhirServer/bulkdata/storageProviders/<source>/auth/typestringA type of hmac, iam, basic or connection
fhirServer/bulkdata/storageProviders/<source>/auth/accessKeyIdstringFor HMAC, API key for accessing COS
fhirServer/bulkdata/storageProviders/<source>/auth/secretAccessKeystringFor HMAC, secret key for accessing COS
fhirServer/bulkdata/storageProviders/<source>/auth/iamApiKeystringFor IAM, API key for accessing IBM COS
fhirServer/bulkdata/storageProviders/<source>/auth/iamResourceInstanceIdstringFor IAM, secret key for accessing IBM COS
fhirServer/bulkdata/storageProviders/<source>/auth/usernamestringFor basic, user COS
fhirServer/bulkdata/storageProviders/<source>/auth/passwordstringFor basic, password for accessing COS
fhirServer/bulkdata/storageProviders/<source>/auth/connectionstringFor Azure Blob Service, the connection string is used
fhirServer/bulkdata/storageProviders/<source>/operationOutcomeProviderstringthe default storage provider used to output Operation Outcomes (file, s3 only)
fhirServer/bulkdata/storageProviders/<source>/accessTypestringThe s3 access type, host or path (s3 only) Link
fhirServer/bulkdata/storageProviders/<source>/requiresAccessTokenbooleancontrols the $bulkdata-status response to indicate Bulk Data storageprovider requires an accessToken using requiresAccessToken. When presigned URLs are enabled, this setting is overridden and shows as false in the $export response.
fhirServer/bulkdata/storageProviders/<source>/allowAllResourcesstringEnables multiple resources to be loaded from a single ndjson.
fhirServer/operations/erase/enabledbooleanEnables the $erase operation
fhirServer/operations/erase/allowedRoleslistThe list of allowed roles, allowed entries are: FHIRUsers every authenticated user, FHIROperationAdmin which is authenticated FHIRAdmin users
fhirServer/operations/membermatch/enabledbooleanEnables or disables the $member-match
fhirServer/operations/membermatch/strategystringThe key identifying the Member Match strategy
fhirServer/operations/membermatch/extendedPropsobjectThe extended options for the extended member match implementation
fhirServer/operations/everything/includeTypeslistThe list of related resource types to include alongside the patient compartment resource types. Instances of these resource types will only be returned when they are referenced from one or more resource instances from the target patient compartment. Example values are like Location, Medication, Organization, and Practitioner
fhirServer/remoteIndexService/typestringThe type of service used to send remote index messages. Only kafka is currently supported
fhirServer/remoteIndexService/instanceIdentifierstringA UUID or other identifier unique to this cluster of LinuxForHealth FHIR Servers
fhirServer/remoteIndexService/kafka/modestringCurrent operation mode of the service. Specify ACTIVE to use the service
fhirServer/remoteIndexService/kafka/topicNamestringThe Kafka topic name. Typically FHIR_REMOTE_INDEX
fhirServer/remoteIndexService/kafka/connectionProperties/bootstrap.serversstringBootstrap servers for the Kafka service
fhirServer/remoteIndexService/kafka/connectionProperties/sasl.jaas.configstringKafka service authentication
fhirServer/remoteIndexService/kafka/connectionProperties/sasl.mechanismstringKafka service authentication
fhirServer/remoteIndexService/kafka/connectionProperties/security.protocolstringKafka service security
fhirServer/remoteIndexService/kafka/connectionProperties/ssl.protocolstringKafka service SSL configuration
fhirServer/remoteIndexService/kafka/connectionProperties/ssl.enabled.protocolsstringKafka service SSL configuration
fhirServer/remoteIndexService/kafka/connectionProperties/ssl.endpoint.identification.algorithmstringKafka service SSL configuration

5.1.2 Default property values

Property NameDefault value
fhirServer/core/defaultPrettyPrintfalse
fhirServer/core/tenantIdHeaderNameX-FHIR-TENANT-ID
fhirServer/core/dataSourceIdHeaderNameX-FHIR-DSID
fhirServer/core/originalRequestUriHeaderNamenull
fhirServer/core/defaultHandlingstrict
fhirServer/core/allowClientHandlingPreftrue
fhirServer/core/checkReferenceTypestrue
fhirServer/core/checkControlCharacterstrue
fhirServer/core/serverRegistryResourceProviderEnabledfalse
fhirServer/core/serverResolveFunctionEnabledfalse
fhirServer/core/conditionalDeleteMaxNumber10
fhirServer/core/capabilityStatementCacheTimeout60
fhirServer/core/extendedCodeableConceptValidationtrue
fhirServer/core/defaultPageSize10
fhirServer/core/maxPageSize1000
fhirServer/core/maxPageIncludeCount1000
fhirServer/core/capabilitiesUrlnull
fhirServer/core/externalBaseUrlnull
fhirServer/core/ifNoneMatchReturnsNotModifiedfalse
fhirServer/core/defaultFhirVersion4.0
fhirServer/core/useImplicitTypeScopingForWholeSystemInteractionstrue
fhirServer/validation/failFastfalse
fhirServer/term/capabilitiesUrlnull
fhirServer/term/cachingDisabledfalse
fhirServer/term/graphTermServiceProviders/enabledfalse
fhirServer/term/graphTermServiceProviders/timeLimit90000
fhirServer/term/remoteTermServiceProviders/enabledfalse
fhirServer/term/remoteTermServiceProviders/hostnameVerificationEnabledtrue
fhirServer/term/remoteTermServiceProviders/httpTimeout60000
fhirServer/resources/opentrue
fhirServer/resources/Resource/interactionsnull (all interactions supported)
fhirServer/resources/Resource/searchParametersnull (all global search parameters supported)
fhirServer/resources/Resource/searchParameters/<code>null
fhirServer/resources/Resource/searchIncludesnull (all _include values supported)
fhirServer/resources/Resource/searchRevIncludesnull (all _revinclude values supported)
fhirServer/resources/Resource/searchParameterCombinationsnull (all search parameter combinations supported)
fhirServer/resources/Resource/profiles/atLeastOnenull (no resource profile assertions required)
fhirServer/resources/Resource/profiles/notAllowednull (any resource profile assertions allowed)
fhirServer/resources/Resource/profiles/allowUnknowntrue
fhirServer/resources/Resource/profiles/defaultVersionsnull (FHIR server determines default versions)
fhirServer/resources/Resource/profiles/defaultVersions/<profile>null
fhirServer/resources/<resourceType>/interactionsnull (inherits from fhirServer/resources/Resource/interactions)
fhirServer/resources/<resourceType>/searchParametersnull (all type-specific search parameters supported)
fhirServer/resources/<resourceType>/searchParameters/<code>null
fhirServer/resources/<resourceType>/searchIncludesnull (inherits from fhirServer/resources/Resource/searchIncludes)
fhirServer/resources/<resourceType>/searchRevIncludesnull (inherits from fhirServer/resources/Resource/searchRevIncludes)
fhirServer/resources/<resourceType>/searchParameterCombinationsnull (inherits from fhirServer/resources/Resource/searchParameterCombinations)
fhirServer/resources/<resourceType>/profiles/atLeastOnenull (inherits from fhirServer/resources/Resource/profiles/atLeastOne)
fhirServer/resources/<resourceType>/profiles/notAllowednull (inherits from fhirServer/resources/Resource/profiles/notAllowed)
fhirServer/resources/<resourceType>/profiles/allowUnknownnull (inherits from fhirServer/resources/Resource/profiles/allowUnknown)
fhirServer/resources/<resourceType>/profiles/defaultVersionsnull (inherits from fhirServer/resources/Resource/profiles/defaultVersions)
fhirServer/resources/<resourceType>/profiles/defaultVersions/<profile>null
fhirServer/notifications/common/includeResourceTypes["*"]
fhirServer/notifications/common/maxNotificationSizeBytes1000000
fhirServer/notifications/common/maxNotificationSizeBehaviorsubset
fhirServer/notifications/websocket/enabledfalse
fhirServer/notifications/kafka/enabledfalse
fhirServer/notifications/kafka/syncfalse
fhirServer/notifications/kafka/topicNamefhirNotifications
fhirServer/notifications/kafka/connectionProperties{}
fhirServer/notifications/nats/enabledfalse
fhirServer/notifications/nats/clusternats-streaming
fhirServer/notifications/nats/channelfhirNotifications
fhirServer/notifications/nats/clientIdfhir-server
fhirServer/notifications/nats/servers
fhirServer/notifications/nats/useTLStrue
fhirServer/notifications/nats/truststoreLocation
fhirServer/notifications/nats/truststorePassword
fhirServer/notifications/nats/keystoreLocation
fhirServer/notifications/nats/keystorePassword
fhirServer/persistence/payload/<datasourceId>/type
fhirServer/persistence/payload/<datasourceId>/connectionProperties
fhirServer/persistence/payload/<datasourceId>/connectionProperties/connectionString
fhirServer/persistence/payload/<datasourceId>/connectionProperties/serviceVersion
fhirServer/persistence/payload/<datasourceId>/connectionProperties/containerName
fhirServer/persistence/factoryClassnameorg.linuxforhealth.fhir.persistence.jdbc.FHIRPersistenceJDBCFactory
fhirServer/persistence/common/updateCreateEnabledtrue
fhirServer/persistence/datasourcesembedded Derby database: derby/fhirDB
fhirServer/persistence/datasources/<datasourceId>/typederby
fhirServer/persistence/datasources/<datasourceId>/jndiNamejndi/fhir_<tenantId>_<datasourceId>
fhirServer/persistence/datasources/<datasourceId>/currentSchemanull
fhirServer/persistence/datasources/<datasourceId>/searchOptimizerOptions/from_collapse_limit16
fhirServer/persistence/datasources/<datasourceId>/searchOptimizerOptions/join_collapse_limit16
fhirServer/search/useBoundingRadiusfalse
fhirServer/search/enableLegacyWholeSystemSearchParamsfalse
fhirServer/security/corstrue
fhirServer/security/basic/enabledfalse
fhirServer/security/certificates/enabledfalse
fhirServer/security/oauth/enabledfalse
fhirServer/security/oauth/regUrl""
fhirServer/security/oauth/authUrl""
fhirServer/security/oauth/tokenUrl""
fhirServer/security/oauth/manageUrl""
fhirServer/security/oauth/introspectUrl""
fhirServer/security/oauth/revokeUrl""
fhirServer/security/oauth/smart/enabledfalse
fhirServer/security/oauth/smart/scopesnull
fhirServer/security/oauth/smart/capabilitiesnull
fhirServer/security/validateBinarySecurityContexttrue
fhirServer/audit/serviceClassName""
fhirServer/audit/serviceProperties/auditTopicFHIR_AUDIT
fhirServer/audit/serviceProperties/geoCityUnknownCity
fhirServer/audit/serviceProperties/geoStateUnknownState
fhirServer/audit/serviceProperties/geoCountyUnknownCountry
fhirServer/audit/serviceProperties/mappercadf
fhirServer/audit/serviceProperties/loadenvironment
fhirServer/bulkdata/validBaseUrlsDisabledfalse
fhirServer/bulkdata/cosFileMaxResources200000
fhirServer/bulkdata/cosFileMaxSize209715200
fhirServer/bulkdata/patientExportPageSize200
fhirServer/bulkdata/useFhirServerTrustStorefalse
fhirServer/bulkdata/ignoreImportOutcomesfalse
fhirServer/bulkdata/enabledtrue
fhirServer/bulkdata/core/api/trustAllfalse
fhirServer/bulkdata/core/cos/partUploadTriggerSizeMB10
fhirServer/bulkdata/core/cos/objectSizeThresholdMB200
fhirServer/bulkdata/core/cos/objectResourceCountThreshold200000
fhirServer/bulkdata/core/cos/requestTimeout120
fhirServer/bulkdata/core/cos/socketTimeout120
fhirServer/bulkdata/core/cos/useServerTruststorefalse
fhirServer/bulkdata/core/cos/presignedExpiry86400
fhirServer/bulkdata/core/azure/objectSizeThresholdMB200
fhirServer/bulkdata/core/azure/objectResourceCountThreshold200000
fhirServer/bulkdata/core/batchIdEncodingKey""
fhirServer/bulkdata/core/pageSize1000
fhirServer/bulkdata/core/maxPartitions5
fhirServer/bulkdata/core/maxInputs5
fhirServer/bulkdata/core/iamEndpointhttps://iam.cloud.ibm.com/oidc/token
fhirServer/bulkdata/core/maxChunkReadTime90000
fhirServer/bulkdata/core/defaultExportProviderdefault
fhirServer/bulkdata/core/defaultImportProviderdefault
fhirServer/bulkdata/core/defaultOutcomeProviderdefault
fhirServer/bulkdata/core/enableSkippableUpdatestrue
fhirServer/bulkdata/storageProviders/<source>/disableBaseUrlValidationfalse
fhirServer/bulkdata/storageProviders/<source>/disableOperationOutcomesfalse
fhirServer/bulkdata/storageProviders/<source>/duplicationCheckfalse
fhirServer/bulkdata/storageProviders/<source>/validateResourcesfalse
fhirServer/bulkdata/storageProviders/<source>/presignedfalse
fhirServer/bulkdata/storageProviders/<source>/createfalse
fhirServer/bulkdata/storageProviders/<source>/accessTypepath
fhirServer/bulkdata/storageProviders/<source>/requiresAccessTokenfalse
fhirServer/bulkdata/storageProviders/<source>/allowAllResourcesfalse
fhirServer/bulkdata/storageProviders/<source>/serviceVersionnull
fhirServer/operations/erase/enabledfalse
fhirServer/operations/erase/allowedRolesempty, all roles
fhirServer/operations/membermatch/enabledtrue
fhirServer/operations/membermatch/strategydefault
fhirServer/operations/membermatch/extendedPropsempty
fhirServer/operations/everything/includeTypesnull
fhirServer/remoteIndexService/typenull
fhirServer/remoteIndexService/instanceIdentifiernull
fhirServer/remoteIndexService/kafka/modenull
fhirServer/remoteIndexService/kafka/topicNamenull
fhirServer/remoteIndexService/kafka/connectionProperties/bootstrap.serversnull
fhirServer/remoteIndexService/kafka/connectionProperties/sasl.jaas.confignull
fhirServer/remoteIndexService/kafka/connectionProperties/sasl.mechanismnull
fhirServer/remoteIndexService/kafka/connectionProperties/security.protocolnull
fhirServer/remoteIndexService/kafka/connectionProperties/ssl.protocolnull
fhirServer/remoteIndexService/kafka/connectionProperties/ssl.enabled.protocolsnull
fhirServer/remoteIndexService/kafka/connectionProperties/ssl.endpoint.identification.algorithmnull

5.1.3 Property attributes

Depending on the context of their use, config properties can be:

  • tenant-specific or global
  • dynamic or static

The following table tracks which properties can be set on a tenant-specific basis and which properties are loaded dynamically. If you change a property that has an N in the Dynamic? column, it means you must restart the server for that change to take effect. Most tenant-specific properties support “fallback” to the default tenant config. Cases where that behavior is not supported are marked below with an N in the Fallback? column.

Property NameTenant-specific?Dynamic?Fallback?
fhirServer/core/defaultPrettyPrintYYY
fhirServer/core/tenantIdHeaderNameNN
fhirServer/core/dataSourceIdHeaderNameNN
fhirServer/core/originalRequestUriHeaderNameNN
fhirServer/core/defaultHandlingYYY
fhirServer/core/allowClientHandlingPrefYYY
fhirServer/core/checkReferenceTypesNN
fhirServer/core/checkControlCharactersNN
fhirServer/core/serverRegistryResourceProviderEnabledNN
fhirServer/core/serverResolveFunctionEnabledNN
fhirServer/core/conditionalDeleteMaxNumberYYY
fhirServer/core/capabilityStatementCacheTimeoutYYY
fhirServer/core/extendedCodeableConceptValidationNN
fhirServer/core/disabledOperationsNN
fhirServer/core/defaultPageSizeYYY
fhirServer/core/ifNoneMatchReturnsNotModifiedYYY
fhirServer/core/maxPageSizeYYY
fhirServer/core/maxPageIncludeCountYYY
fhirServer/core/capabilitiesUrlYYY
fhirServer/core/externalBaseUrlYYY
fhirServer/core/defaultFhirVersionYYY
fhirServer/core/useImplicitTypeScopingForWholeSystemInteractionsYYY
fhirServer/validation/failFastYYY
fhirServer/term/cachingDisabledNN
fhirServer/term/graphTermServiceProviders/enabledNN
fhirServer/term/graphTermServiceProviders/timeLimitNN
fhirServer/term/graphTermServiceProviders/configurationNN
fhirServer/term/remoteTermServiceProviders/enabledNN
fhirServer/term/remoteTermServiceProviders/baseNN
fhirServer/term/remoteTermServiceProviders/trustStoreNN
fhirServer/term/remoteTermServiceProviders/hostnameVerificationEnabledNN
fhirServer/term/remoteTermServiceProviders/basicAuthNN
fhirServer/term/remoteTermServiceProviders/headersNN
fhirServer/term/remoteTermServiceProviders/httpTimeoutNN
fhirServer/term/remoteTermServiceProviders/supportsNN
fhirServer/term/capabilitiesUrlYYY
fhirServer/resourcesYYY
fhirServer/resources/openYYN
fhirServer/resources/Resource/interactionsYYN
fhirServer/resources/Resource/searchParametersYYN
fhirServer/resources/Resource/searchParameters/<code>YYN
fhirServer/resources/Resource/searchIncludesYYN
fhirServer/resources/Resource/searchRevIncludesYYN
fhirServer/resources/Resource/searchParameterCombinationsYYN
fhirServer/resources/Resource/profiles/atLeastOneYYN
fhirServer/resources/Resource/profiles/notAllowedYYN
fhirServer/resources/Resource/profiles/allowUnknownYYN
fhirServer/resources/Resource/profiles/defaultVersionsYYN
fhirServer/resources/Resource/profiles/defaultVersions/<profile>YYN
fhirServer/resources/<resourceType>/interactionsYYN
fhirServer/resources/<resourceType>/searchParametersYNN
fhirServer/resources/<resourceType>/searchParameters/<code>YNN
fhirServer/resources/<resourceType>/searchIncludesYYN
fhirServer/resources/<resourceType>/searchRevIncludesYYN
fhirServer/resources/<resourceType>/searchParameterCombinationsYYN
fhirServer/resources/<resourceType>/profiles/atLeastOneYYN
fhirServer/resources/<resourceType>/profiles/notAllowedYYN
fhirServer/resources/<resourceType>/profiles/allowUnknownYYN
fhirServer/resources/<resourceType>/profiles/defaultVersionsYYN
fhirServer/resources/<resourceType>/profiles/defaultVersions/<profile>YYN
fhirServer/notifications/common/includeResourceTypesNN
fhirServer/notifications/common/maxNotificationSizeBytesYYY
fhirServer/notifications/common/maxNotificationSizeBehaviorYYY
fhirServer/notifications/websocket/enabledNN
fhirServer/notifications/kafka/enabledNN
fhirServer/notifications/kafka/topicNameNN
fhirServer/notifications/kafka/connectionPropertiesNN
fhirServer/notifications/kafka/syncYYY
fhirServer/notifications/nats/enabledNN
fhirServer/notifications/nats/clusterNN
fhirServer/notifications/nats/channelNN
fhirServer/notifications/nats/clientIdNN
fhirServer/notifications/nats/serversNN
fhirServer/notifications/nats/useTLSNN
fhirServer/notifications/nats/truststoreLocationNN
fhirServer/notifications/nats/truststorePasswordNN
fhirServer/notifications/nats/keystoreLocationNN
fhirServer/notifications/nats/keystorePasswordNN
fhirServer/persistence/payload/<datasourceId>/typeYNN
fhirServer/persistence/payload/<datasourceId>/connectionPropertiesYNN
fhirServer/persistence/payload/<datasourceId>/connectionProperties/connectionStringYNN
fhirServer/persistence/payload/<datasourceId>/connectionProperties/serviceVersionYNN
fhirServer/persistence/payload/<datasourceId>/connectionProperties/containerNameYNN
fhirServer/persistence/factoryClassnameNN
fhirServer/persistence/common/updateCreateEnabledNN
fhirServer/persistence/datasourcesYNN
fhirServer/persistence/datasources/<datasourceId>/typeYNN
fhirServer/persistence/datasources/<datasourceId>/jndiNameYYN
fhirServer/persistence/datasources/<datasourceId>/currentSchemaYYN
fhirServer/persistence/datasources/<datasourceId>/searchOptimizerOptions/from_collapse_limitYYN
fhirServer/persistence/datasources/<datasourceId>/searchOptimizerOptions/join_collapse_limitYYN
fhirServer/search/useBoundingRadiusYYY
fhirServer/search/enableLegacyWholeSystemSearchParamsYYY
fhirServer/security/corsYYY
fhirServer/security/basic/enabledYYY
fhirServer/security/certificates/enabledYYY
fhirServer/security/oauth/enabledYYY
fhirServer/security/oauth/regUrlYYY
fhirServer/security/oauth/authUrlYYY
fhirServer/security/oauth/tokenUrlYYY
fhirServer/security/oauth/manageUrlYYY
fhirServer/security/oauth/introspectUrlYYY
fhirServer/security/oauth/revokeUrlYYY
fhirServer/security/oauth/smart/enabledYYY
fhirServer/security/oauth/smart/scopesYYY
fhirServer/security/oauth/smart/capabilitiesYYY
fhirServer/security/validateBinarySecurityContextYYY
fhirServer/audit/serviceClassNameNN
fhirServer/audit/serviceProperties/auditTopicNN
fhirServer/audit/serviceProperties/geoCityNN
fhirServer/audit/serviceProperties/geoStateNN
fhirServer/audit/serviceProperties/geoCountyNN
fhirServer/audit/serviceProperties/mapperNN
fhirServer/audit/serviceProperties/loadNN
fhirServer/audit/hostnameNN
fhirServer/audit/ipNN
fhirServer/bulkdata/enabledYYY
fhirServer/bulkdata/core/api/urlYYY
fhirServer/bulkdata/core/api/userYYY
fhirServer/bulkdata/core/api/passwordYYY
fhirServer/bulkdata/core/api/truststoreYYY
fhirServer/bulkdata/core/api/truststorePasswordYYY
fhirServer/bulkdata/core/api/trustAllYYY
fhirServer/bulkdata/core/cos/partUploadTriggerSizeMBNN
fhirServer/bulkdata/core/cos/objectSizeThresholdMBNN
fhirServer/bulkdata/core/cos/objectResourceCountThresholdNN
fhirServer/bulkdata/core/cos/requestTimeoutNN
fhirServer/bulkdata/core/cos/socketTimeoutNN
fhirServer/bulkdata/core/cos/useServerTruststoreYYY
fhirServer/bulkdata/core/cos/presignedExpiryYYY
fhirServer/bulkdata/core/azure/objectSizeThresholdMBNN
fhirServer/bulkdata/core/azure/objectResourceCountThresholdNN
fhirServer/bulkdata/core/batchIdEncodingKeyYNY
fhirServer/bulkdata/core/pageSizeYYY
fhirServer/bulkdata/core/maxPartitionsYYY
fhirServer/bulkdata/core/maxInputsYYY
fhirServer/bulkdata/core/iamEndpointNN
fhirServer/bulkdata/core/fastTxTimeoutNN
fhirServer/bulkdata/core/defaultExportProviderYYY
fhirServer/bulkdata/core/defaultImportProviderYYY
fhirServer/bulkdata/core/defaultOutcomeProviderYYY
fhirServer/bulkdata/core/enableSkippableUpdatesYYY
fhirServer/bulkdata/storageProviders/<source>/typeYYY
fhirServer/bulkdata/storageProviders/<source>/bucketNameYYY
fhirServer/bulkdata/storageProviders/<source>/locationYYY
fhirServer/bulkdata/storageProviders/<source>/endpointInternalYYY
fhirServer/bulkdata/storageProviders/<source>/endpointExternalYYY
fhirServer/bulkdata/storageProviders/<source>/fileBaseYYY
fhirServer/bulkdata/storageProviders/<source>/validBaseUrlsYYY
fhirServer/bulkdata/storageProviders/<source>/disableBaseUrlValidationYYY
fhirServer/bulkdata/storageProviders/<source>/disableOperationOutcomesYYY
fhirServer/bulkdata/storageProviders/<source>/duplicationCheckYYY
fhirServer/bulkdata/storageProviders/<source>/validateResourcesYYY
fhirServer/bulkdata/storageProviders/<source>/presignedYYY
fhirServer/bulkdata/storageProviders/<source>/createYYY
fhirServer/bulkdata/storageProviders/<source>/auth/typeYYY
fhirServer/bulkdata/storageProviders/<source>/auth/accessKeyIdYYY
fhirServer/bulkdata/storageProviders/<source>/auth/secretAccessKeyYYY
fhirServer/bulkdata/storageProviders/<source>/auth/iamApiKeyYYY
fhirServer/bulkdata/storageProviders/<source>/auth/iamResourceInstanceIdYYY
fhirServer/bulkdata/storageProviders/<source>/auth/usernameYYY
fhirServer/bulkdata/storageProviders/<source>/auth/passwordYYY
fhirServer/bulkdata/storageProviders/<source>/auth/connectionYYY
fhirServer/bulkdata/storageProviders/<source>/operationOutcomeProviderYYY
fhirServer/bulkdata/storageProviders/<source>/accessTypeYYY
fhirServer/bulkdata/storageProviders/<source>/requiresAccessTokenYYY
fhirServer/bulkdata/storageProviders/<source>/allowAllResourcesYYY
fhirServer/bulkdata/storageProviders/<source>/serviceVersionYYY
fhirServer/operations/erase/enabledYYY
fhirServer/operations/erase/allowedRolesYYY
fhirServer/operations/membermatch/enabledYYY
fhirServer/operations/membermatch/strategyYYY
fhirServer/operations/membermatch/extendedPropsYYY
fhirServer/operations/everything/includeTypesYYN
fhirServer/remoteIndexService/typeNNN
fhirServer/remoteIndexService/instanceIdentifierNNN
fhirServer/remoteIndexService/kafka/modeNNN
fhirServer/remoteIndexService/kafka/topicNameNNN
fhirServer/remoteIndexService/kafka/connectionProperties/bootstrap.serversNNN
fhirServer/remoteIndexService/kafka/connectionProperties/sasl.jaas.configNNN
fhirServer/remoteIndexService/kafka/connectionProperties/sasl.mechanismNNN
fhirServer/remoteIndexService/kafka/connectionProperties/security.protocolNNN
fhirServer/remoteIndexService/kafka/connectionProperties/ssl.protocolNNN
fhirServer/remoteIndexService/kafka/connectionProperties/ssl.enabled.protocolsNNN
fhirServer/remoteIndexService/kafka/connectionProperties/ssl.endpoint.identification.algorithmNNN

5.2 Keystores, truststores, and the LinuxForHealth FHIR Server

5.2.1 Background

As stated earlier, the FHIR server is installed with a default configuration in server.xml which includes the definition of a keystore (fhirKeyStore.p12) and a truststore (fhirTrustStore.p12)7. These files are provided only as examples and while they may suffice in a test environment, the FHIR server deployer should generate a new keystore and truststore for any installations where security is a concern. Review the information in the following topics to learn how to configure a secure keystore and truststore.

Additionally, the server has a trustDefault.xml config dropin that references the SEC_TLS_TRUSTDEFAULTCERTS variable (defaultValue = true) to indicate whether or not the JVM truststore should be used in combination with the configured trust store.

5.2.2 WebApp security

By default, the FHIR server REST API is only available via HTTPS on port 9443 and is protected by HTTP basic authentication. Alternatively, the server can use OpenID Connect and OAuth 2.0 via a Bearer Token as described in Section 5.3 OpenID Connect and OAuth 2.0. In addition, the FHIR server web application can be secured via client certificate-based authentication.

Here are some notes related to these authentication schemes:

  • Basic authentication is a very simple authentication scheme and should only be used over HTTPS because the username and password are essentially transmitted in plain text.
  • OAuth 2.0 authentication can only be used in conjunction with an HTTPS endpoint because the OAuth authorization steps rely on SSL handshake negotiations.
  • Client certificate-based authentication can only be used in conjunction with an HTTPS endpoint since it involves SSL handshake negotiations. The main value of client authentication is that the server is able to securely authenticate the client through the use of certificates.

5.2.3 Configuring mutual TLS authentication

To properly configure the FHIR server’s keystore and truststore files, perform the following steps.

5.2.3.1 Configure the keyStores

  1. Create a new self-signed server certificate8 and store it in a new keystore file located in the <WLP_HOME>/usr/servers/fhir-server/resources/security directory.

    In these instructions, we’ll call this file serverKeystore.jks, although you can name your server keystore file anything you choose. We’ll use the keytool9 command for all keystore- and truststore-related steps, although there are several ways to perform these actions.

    The following command will generate a new self-signed certificate and store it in serverKeystore.jks:

    keytool -keystore serverKeystore.jks -storepass change-password -genkey
    -alias default -keyalg RSA -keypass change-password
  2. Export the server certificate so that it can be imported into the client’s truststore:

    keytool -keystore serverKeystore.jks -storepass change-password -export
    -alias default -file server-public-key.cer
  3. Create the client’s certificate and store it in clientKeystore.jks:

    keytool -keystore clientKeystore.jks -storepass change-password -genkey
    -alias client-auth -keyalg RSA -keypass change-password

    Note: keytool will prompt you for the various components of the distinguished name (DN) associated with the certificate (similar to Step 1). The value that you specify for the common name (CN) component of the DN must match a username in the basic user registry10 configured within the server.xml file. This step is crucial for the client certificate-based authentication to work properly. The whole point of this authentication scheme is for the client to transmit its identity to the server via the client certificate, and the client’s username must be contained in that certificate (the CN component of the DN) so that the FHIR server can properly authenticate the client.

  4. Export the client’s certificate so that it can be imported into the server’s truststore:

    keytool -keystore clientKeystore.jks -storepass change-password -export -alias client-auth -file client-public-key.cer
  5. Import the server’s public key certificate into the client’s truststore:

    keytool -keystore clientTruststore.jks -storepass change-password -import -file server-public-key.cer
  6. Import the client’s public key certificate into the server’s truststore:

    keytool -keystore serverTruststore.jks -storepass change-password -import -file client-public-key.cer

At this point, you should have a client keystore that contains a client certificate whose Distinguished Name’s Common Name component is set to the username. You should also have a client truststore which contains the server’s public key certificate. Essentially, the server and client both have a keystore that contains their own private and public key certificate and they both have a truststore which contains the public key certificate of their counterpart.

5.2.3.1 Configure the server

Copy the server keystore (serverKeystore.jks) and truststore (serverTruststore.jks) files to the appropriate directory (<WLP_HOME>/usr/servers/fhir-server/resources/security). Then configure the server.xml file correctly to reference your new keystore and truststore files.

5.2.3.2 Configure the client

The precise steps required to configure certificate-based authentication for a client application depend on the specific REST API client framework, but these are the general rules:

  • If the client is using the FHIR server’s HTTPS endpoint, then the client’s truststore should be configured with the certificate of the FHIR server11.
  • If the client is using basic authentication, then it must send an appropriate Authorization request header containing the username and password information in the HTTP request.
  • If the client is using client certificate-based Authentication, then the client keystore must be configured with a certificate that is trusted by the FHIR server12.
  • If the client is using OAuth 2.0 Authentication, then the client keystore must be configured with the REST API client framework. In addition, it must send an appropriate Authorization request header containing the Bearer token in the HTTP request.

5.3 OpenID Connect and OAuth 2.0

The FHIR specification recommends the use of OAuth 2.0. The LinuxForHealth FHIR Server supports OAuth 2.0 through the use of WebSphere Liberty / OpenLiberty features.

While it is possible to configure Liberty as an OpenID Connect Client, more typically the LinuxForHealth FHIR Server will be configured as a generic OAuth 2.0 “Protected Resource Server” that works with JWT access tokens that have been issued by a trusted Authorization Server like Keycloak.

5.3.1 Configure Liberty to be an OAuth 2.0 Protected Resource Server

Liberty can be configured to act as an OAuth 2.0 Protected Resource Server via either the openidConnectClient feature or the mpJwt feature.

One advantage of the mpJwt approach is that users can be mapped into pre-defined JEE security roles. To enable this feature without modifying the default server.xml, move the jwtRS.xml config snippet from configDropins/disabled/ to configDropins/defaults/ and modify as desired.

A copy of this snippet is provided here for illustrative purposes:

<server description="fhir-server">
<featureManager>
<feature>mpJwt-1.1</feature>
</featureManager>
<!-- Override the application-bnd binding of the main webapp -->
<webApplication contextRoot="fhir-server/api/v4" id="fhir-server-webapp" location="fhir-server.war" name="fhir-server-webapp">
<application-bnd id="bind">
<security-role id="users" name="FHIRUsers">

In the snippet above, the mpJwt element is configured to obtain JWK information from http://keycloak:8080/auth/realms/test/protocol/openid-connect/certs and use this to validate JWT tokens that are passed to the server.

Additionally, the server will validate the iss (issuer) and aud (audiences) claims of the JWT and use the sub claim as the user principal (for audit logging).

Finally, the value(s) of the group claim are used to map this user into a corresponding JEE security-role as defined in the application-bnd section of the webApplication element.

5.3.2 Advertise the OAuth endpoints via fhir-server-config

To make the FHIR Server advertise the OAuth endpoints of the configured provider, supply values for at least the following properties in the default fhir-server-config.json file:

  • fhirServer/security/oauth/authUrl
  • fhirServer/security/oauth/tokenUrl

These values will be used to populate the corresponding entries in both the server capability statement (GET [base]/metadata) and the smart-configuration (GET [base]/.well-known/smart-configuration).

For example, the following excerpt from a CapabilityStatement shows sample OAuth-related URLs (register, authorize, and token) values in the valueUri elements.

"rest": [
{
"mode": "server",
"security": {
"extension": [
{
"url": "http://fhir-registry.smarthealthit.org/StructureDefinition/oauth-uris"
"extension": [

SMART on FHIR applications should use the .well-known/smart-configuration endpoint to determine the OAuth URLs to use for authorization, but the entries in the Capability Statement are needed for backwards compatibility.

5.3.3 SMART App Launch

To support SMART App Launch, the LinuxForHealth FHIR Server can be used with a SMART-enabled authorization server. For an example of a SMART-enabled Authorization Server, see the Alvearie Keycloak extensions for FHIR.

The OAuth configuration described in the previous sections will restrict API access to clients with a valid access token. However, SMART defines additional access controls via OAuth 2.0 scopes and context parameters.

To enforce authorization policy on the server, drop the fhir-smart module into the server’s userlib directory.

This component uses the LinuxForHealth FHIR Server’s PersistenceInterceptor feature to automatically scope searches to the compartments for which the user has access (as indicated by a special patient_id claim in the access token).

Additionally, before returning resources to the client, the fhir-smart component performs authorization policy enforcement based on the list of SMART scopes included in the token’s scope claim and the list of patient compartments in the patient_id claim.

When the HTTP header Prefer: return=minimal is specified on a search or history request, only minimal resource metadata is retrieved. In those cases, either user or system SMART scopes must be used, since the resource data necessary to enforce access via patient SMART scopes is not available.

For an example of using the LinuxForHealth FHIR Server together with a SMART-enabled Keycloak authorization server, please see the data-access pattern at https://github.com/LinuxForHealth/health-patterns/tree/main/data-access.

5.4 Custom HTTP Headers

The LinuxForHealth FHIR Server supports the following custom HTTP Headers:

Header NameDescription
X-FHIR-TENANT-IDSpecifies which tenant config should be used for the request. Default is default. The header name can be overridden via config property fhirServer/core/tenantIdHeaderName.
X-FHIR-DSIDSpecifies which datastore config should be used for the request. Default is default. The header name can be overridden via config property fhirServer/core/dataSourceIdHeaderName.
X-FHIR-FORWARDED-URLThe original (user-facing) request URL; used for constructing absolute URLs within the server response. Only enabled when explicitly configured in the default fhir-server-config.json. If either the config property or the header itself is missing, the server will use the actual request URL. The header name can be overridden via config property fhirServer/core/originalRequestUriHeaderName. Note that fhirServer/core/externalBaseUrl overrides the X-FHIR-FORWARDED-URL and is used to construct the absolute URL. Also note that the base URL’s value must not include a path segment that matches any FHIR resource type name (case-sensitive). For example, ”https://example.com” or ”https://example.com/my/patient/api” are fine, but ”https://example.com/my/Patient/api” is not.
X-FHIR-FORCE-UPDATEBy default, when the server receives an update request, it performs a resource comparison and only performs the update if the contents of the resource have changed. Set this header to true to skip that check and perform a normal update (i.e. create a new version for this resource id).

6 Related topics

For more information about topics related to configuring a FHIR server, see the following documentation:


  • 1

    The fhir-server-config.json file contains configuration information associated with the FHIR server. The global configuration is located in WLP_HOME/wlp/usr/servers/fhir-server/config/default/fhir-server-config.json, with tenant-specific configuration contained in config/TENANT_ID/fhir-server-config.json.

  • 2

    The names of these request headers are configurable within the FHIR server’s fhir-server-config.json file. For more information, see Section 5.1 Configuration properties reference.

  • 3

    For more information on multi-tenant support, including multi-tenant configuration properties, jump to Section 4.9 Multi-Tenancy.

  • 4

    An external reference is a reference to a resource which is meaningful outside a particular request bundle. The value typically includes the resource type and the resource identifier, and could be an absolute or relative URL. Examples: https://fhirserver1:9443/fhir-server/api/v4/Patient/12345, Patient/12345, etc. Requiring relative URLs to include a valid resource type can be configured via the fhirServer/core/checkReferenceTypes config property. For more information, see Section 5.1 Configuration properties reference.

  • 5

    A local reference is a reference used within a request bundle that refers to another resource within the same request bundle and is meaningful only within that request bundle. A local reference starts with urn:.

  • 6

    Keystore and truststore files have the same basic structure. They both provide a secure means for storing certificates. Typically, we think of a keystore as a file that contains certificates that consist of a private/public key pair, whereas a truststore contains certificates that consist of a public key or trusted certificates.

  • 7

    While the instructions here show examples of creating self-signed certificates, in reality the FHIR Server deployer will likely need to use certificates that have been signed by a Certificate Authority (CA) such as Verisign, etc.

  • 8

    The keytool command is provided as part of the Java 11 JRE. The command can be found in $JAVA_HOME/jre/bin.

  • 9 These instructions assume the use of a basic user registry in the server.xml file. If you are instead using an LDAP registry, then the entire DN associated with the client certificate must match the DN of a user in the LDAP registry. [↩](#a10)
  • 10

    For the JAX-RS 2.0 Client API, you would call the ClientBuilder.truststore() method.

  • 11

    For the JAX-RS 2.0 Client API, you would call the ClientBuilder.keystore() method.


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