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issue #1708 updated docs per review comments
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Signed-off-by: Robin Arnold <robin.arnold23@ibm.com>
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punktilious committed Nov 22, 2020
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## 2.1 Installing a new server
0. Prereqs: The IBM FHIR Server requires Java 8 or higher and has been tested with OpenJDK 8, OpenJDK 11, and the IBM SDK, Java Technology Edition, Version 8. To install Java on your system, we recommend downloading and installing OpenJDK 8 from https://adoptopenjdk.net/.

1. To install the FHIR server, build or download the `fhir-install` zip installer (e.g. `fhir-server-distribution.zip` or `fhir-install-4.0.0-rc1-20191014-1610`).
1. To install the IBM FHIR Server, build or download the `fhir-install` zip installer (e.g. `fhir-server-distribution.zip` or `fhir-install-4.0.0-rc1-20191014-1610`).
The Maven build creates the zip package under `fhir-install/target`. Alternatively, releases will be made available from the [Releases tab](https://github.com/ibm/fhir/releases).

2. Unzip the `.zip` package into a clean directory (referred to as `fhir-installer` here):
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unzip fhir-server-distribution.zip
```
3. Determine an install location for the OpenLiberty server and the FHIR server webapp. Example: `/opt/ibm/fhir-server`
3. Determine an install location for the OpenLiberty server and the IBM FHIR Server webapp. Example: `/opt/ibm/fhir-server`
4. 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 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`.
This step installs the OpenLiberty runtime and the IBM 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`.
5. 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 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](#52-keystores-truststores-and-the-fhir-server).
* Configure a server keystore and truststore. The IBM 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](#52-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](https://openliberty.io/guides/security-intro.html#configuring-the-user-registry).
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`.
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For more information about the capabilities of the implementation, see [Conformance](https://ibm.github.io/FHIR/Conformance).
## 2.2 Upgrading an existing server
The FHIR server does not include an upgrade installer. To upgrade a server to the next version, you can run the installer on a separate server, and then copy the resulting configuration files over to the existing server.
The IBM FHIR Server does not include an upgrade installer. To upgrade a server to the next version, you can run the installer on a separate server, and then copy the resulting configuration files over to the existing server.
To manage database updates over time, the 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 and apply any new changes that are needed to bring the database to the current level.
To manage database updates over time, the IBM 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 and apply any new changes that are needed to bring the database to the current level.
Complete the following steps to upgrade the server:
Expand All @@ -131,7 +131,7 @@ The IBM FHIR Server includes a Docker image [ibmcom/ibm-fhir-server](https://hub
Note, logging for the IBM FHIR Server docker image is to stderr and stdout, and is picked up by Logging agents.
# 3 Configuration
This chapter contains information about the various ways in which the FHIR server can be configured by users.
This chapter contains information about the various ways in which the IBM FHIR Server can be configured by users.
## 3.1 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.
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## 3.3.1 Compartment Search Performance
The IBM FHIR Server now supports the ability to compute and store compartment membership values during ingestion. Once stored, these values can help accelerate compartment-related search queries. To use this feature, update the IBM FHIR Server at least version 4.5.1 and run a reindex operation as described in the release notes for Release 4.5.0. The reindex operation reprocesses the resources stored in the database, computing and storing the new compartment reference values. After the reindex operation has completed, add the `useStoredCompartmentParam` configuration element to the relevant tenant fhir-server-config.json file to allow the search queries to use the pre-computed values:
The IBM FHIR Server supports the ability to compute and store compartment membership values during ingestion. Once stored, these values can help accelerate compartment-related search queries. To use this feature, update the IBM FHIR Server to at least version 4.5.1 and run a reindex operation as described in the [fhir-bucket](https://github.com/IBM/FHIR/tree/master/fhir-bucket) project [README](https://github.com/IBM/FHIR/blob/master/fhir-bucket/README.md). The reindex operation reprocesses the resources stored in the database, computing and storing the new compartment reference values. After the reindex operation has completed, add the `useStoredCompartmentParam` configuration element to the relevant tenant fhir-server-config.json file to allow the search queries to use the pre-computed values:
```
{
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}
}
```
Note that this parameter only enables or disables the compartment search query optimization feature. The compartment membership values are always computed and stored during ingestion or reindexing, regardless of the setting of this value. After the reindex operation is complete, it is recommended to set `useStoredCompartmentParam` to true. No reindex is required if this value is subsequently set to false.
## 3.4 Persistence layer configuration
The IBM 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, IBM Db2, and PostgreSQL. However, Apache Derby is not recommended for production usage.
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