fhir-loader/scripts

FHIR-Bulk Loader Getting Started with Deploy Scripts

In this document, we go over the deploy scripts necessary for installing FHIR Bulk Loader. We cover the order of script execution and the steps to complete the install.

Errata

There are no open issues at this time.

Prerequisites

These scripts will gather (and export) information necessary for the proper deployment and configuration of FHIR Bulk Loader. Credentials and other secure information will be stored in the existing Key Vault attached to your FHIR Service/FHIR Proxy deployment.

• User must have FHIR Server (OSS)/Azure API for FHIR/Azure Healthcare APIs FHIR Service already deployed. Enable FHIR-Proxy if required.
• User must have rights to deploy resources at the Azure Subscription scope (i.e., Contributor role or above).

Note: FHIR Service and FHIR-Proxy use a Key Vault for securing Service Client credentials. Because the deployFhirBulk.bash script scans the Key Vault for FHIR Service and FHIR-Proxy values, only one Key Vault should be used in your Resource Group. If multiple Key Vaults have been deployed in your Resource Group, please use the backup and restore option to copy values to one Key Vault.

Note: The FHIR-Bulk Loader & Export scripts are designed and tested for the Azure Cloud Shell - Bash Shell environment.

Naming & Tagging

All Azure resource types have a scope in which resource names must be unique. Some resource names, such as PaaS services with public endpoints, have global scopes and therefore must be unique across the entire Azure platform. Our deployment scripts suggest naming standards that group logical connections while aligning with Azure best practices. Users are prompted to accept a default name or supply their own names during installation. See below for the FHIR Bulk Loader resource naming convention.

Resource Type	Deploy App Name	Number	Resource Name Example (automatically generated)
sfb-	bulk	random	sfb-bulk123456

Azure Resources deployed with this script are automatically tagged with their origin and deployment name (see example below). Users are able to add/change Tags after installation.

Origin	Deployment
HealthArchitectures	FHIR-Bulk

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Getting Started

Please note you should deploy these components into a tenant and subscription where you have appropriate permissions to create and manage Application Registrations (ie Application Adminitrator RBAC Role or Global Administrator in AAD), and can deploy Resources at the Subscription Scope.

Launch Azure Cloud Shell (Bash Environment)

CTRL+click (Windows or Linux) or CMD+click (Mac) to open in a new window or tab

Clone the repo to your Bash Shell (CLI) environment

git clone https://github.com/microsoft/fhir-loader 

Change working directory to the repo Scripts directory

cd $HOME/fhir-loader/scripts

Make the Bash Shell Scripts used for Deployment and Setup executable

chmod +x *.bash 

Step 1. deployFhirBulk.bash

This is the main component deployment script for the FHIR Bulk Loader Azure components and application code. Note that retry logic is used to account for provisioning delays (e.g., networking provisioning is taking some extra time). Default retry logic is 5 retries.

Ensure you are in the proper directory

cd $HOME/fhir-loader/scripts

Launch the deployFhirBulk.bash shell script

./deployFhirBulk.bash 

Optionally the deployment script can be used with command line options

./deployFhirBulk.bash -i <subscriptionId> -g <resourceGroupName> -l <resourceGroupLocation> -n <deployPrefix> -k <keyVaultName> -o <fhir or proxy>

Optional Parameters details:-

• subscriptionId - The unique identifier for your Azure subscription.
• resourceGroupName - Name of the Resource Group where all the resources will be deployed.
• resourceGroupLocation - Location where the resources will be deployed.
• deployPrefix - This prefix will be appended to all the resources created while deployment.
• keyVaultName - Name of the Key Vault which will be created while deployment.
• fhir or proxy - Use proxy if Smart on FHIR Proxy is enabled; otherwise, use fhir when running the script.

Azure Components installed

• Function App with App Insights and Storage
• Function App Service plan
• EventGrid
• Storage Account (with containers/queues)
• Keyvault (if none exist)

Information needed by this script

• Subscription
• Resource Group Name and Location
• Keyvault Name

This script prompts users for the existing Key Vault name, searches for FHIR Service values in the Key Vault, and if found, loads them. Otherwise the script prompts users for the FHIR Service

• Client ID
• Resource
• Tenant Name
• URL

The deployment script connects the Event Grid System Topics with the respective function app

FHIR-Loader Connections

Event Grid System Topic	Connects to Function App	Located
ndjsoncreated	ImportNDJSON	EventGrid
bundlecreated	ImportBundleEventGrid	EventGrid

FHIR-Loader Application Configuration values loaded by this script

Name	Value	Located
APPINSIGHTS_INSTRUMENTATIONKEY	GUID	App Service Config
AzureWebJobsStorage	Endpoint	App Service Config
FUNCTIONS_EXTENSION_VERSION	Function Version	App Service Config
FUNCTIONS_WORKER_RUNTIME	Function runtime	App Service Config
FBI-TRANSFORMBUNDLES	True (transaction->batch)	App Service Config
FS-URL	FHIR Service URL	App Service Config
SA-FHIR-USEMSI	MSI Identity value	App Service Config
FBI-STORAGEACCT	Storage Connection	Keyvault reference
FS-CLIENT-ID	FHIR Service Client ID	Keyvault reference
FS-SECRET	FHIR Service Client Secret	Keyvault reference
FS-TENANT-NAME	FHIR Service TENANT ID	Keyvault reference
FS-RESOURCE	FHIR Service Resource ID	Keyvault reference

FHIR-Loader - Application Configuration values - unique values

Name	Value	Used For
AzureWebJobs.ImportBundleBlobTrigger.Disabled	1	Prevents Conflicts wit Event Grid
FBI-POOLEDCON-MAXCONNECTIONS	20	Limits service timeouts
WEBSITE_RUN_FROM_PACKAGE	1	Optional - sets app to read only

Upgrade from previous fhir-loader

If you are upgrading from a previous version of fhir-loader you will need to redeploy using the instructions in step 1. of this document. New infrastructure components were added to the fhir-loader