Skip to content

Latest commit

 

History

History
135 lines (97 loc) · 7.28 KB

Readme.md

File metadata and controls

135 lines (97 loc) · 7.28 KB
Raw

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 and set up with FHIR-Proxy.
  • 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

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

Launch Azure Shell

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>

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