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Description

Samples for Microsoft FHIR Server for Azure

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FHIR Server Samples

This respository contains example applications and scenarios that show use of the FHIR Server for Azure and the Azure API for FHIR.

The scenario is meant to illustrate how to connect a web application to the FHIR API. The scenario also illustrates features such as the SMART on FHIR Active Directory Proxy. It can be deployed using the Azure API for FHIR PaaS server:

Or the open source FHIR Server for Azure:

In both cases a storage account will be deploy and in this storage account there is a BLOB container called

fhirimport
, patient bundles generated with Synthea can dumped in this storage container and they will be ingested into the FHIR server. The bulk ingestion is performed by an Azure Function.

The environments can also optionally be configured to support

$export
. To enable

$export
, add the
-EnableExport $true
parameter to the script below. The
$export
operation will produce a new line delimited json (ndjson) for each resource type. These ndjson files are easily consumed with something like Databricks (Apache-Spark). Please see the analytics folder for some details and example queries. Note that the Databricks environment is not deployed automatically with the sandbox and must be set up separately.

Note: To enable

$export
you must have subscription rights that allow you to set data plane access roles for storage accounts, e.g. you must be a subscription owner.

Prerequisites

Before deploying the samples scenario, make sure you have

Az
and
AzureAd
powershell modules installed:
Install-Module Az
Install-Module AzureAd

The new

Az
module requires PowerShell version 5.1 or above installed on your computer. So if you have PowerShell version below 5.1, you need to update it. To check your PowerShell version, you can run:
PowerShell
$PSVersionTable.PSVersion
Currently, there is a bug with PowerShell Az Module version 4.6.1 confirmed with Azure ARM team. For now, please avoid using version 4.6.1. Version 4.5 and versions 4.7.0 or above should work fine. To check your Az module version, you can run:
PowerShell
Get-InstalledModule -Name Az

Deployment

To deploy the sample scenario, first clone this git repo and find the deployment scripts folder:

git clone https://github.com/Microsoft/fhir-server-samples
cd fhir-server-samples/deploy/scripts

Log into your Azure subscription:

Login-AzAccount

Connect to Azure AD with:

Connect-AzureAd -TenantDomain 

NOTE The connection to Azure AD can be made using a different tenant domain than the one tied to your Azure subscription. If you don't have privileges to create app registrations, users, etc. in your Azure AD tenant, you can create a new one, which will just be used for demo identities, etc.

Then, deploy the scenario with the Open Source FHIR Server for Azure:

.\Create-FhirServerSamplesEnvironment.ps1 -EnvironmentName  -UsePaaS $false

or the managed Azure API for FHIR:

.\Create-FhirServerSamplesEnvironment.ps1 -EnvironmentName  -UsePaaS $true

and to enable

$export
:
.\Create-FhirServerSamplesEnvironment.ps1 -EnvironmentName  -UsePaaS $true -EnableExport $true

To delete the senario:

.\Delete-FhirServerSamplesEnvironment.ps1 -EnvironmentName 

NOTE If you are using PowerShell Core on other platforms (macOS or Linux), please make sure to specify password in the command. You can do this by:

./Create-FhirServerSamplesEnvironment.ps1 -EnvironmentName  -UsePaaS  -AdminPassword $(ConvertTo-SecureString -AsPlainText -Force "")

If the deployment is successful, you would see information like below being written on your terminal or CloudShell as the scripts run: ```PowerShell Current context is user: xxxx FhirServer PS module is loaded Current context is user: xxxx Adding permission to keyvault for xxxx Ensuring API application exists Checking if UserPrincipalName exists User not, will create.

DeploymentName : xxxx ResourceGroupName : xxxx ProvisioningState : Succeeded Timestamp : 11/24/2020 10:30:18 PM Mode : Incremental TemplateLink : Uri : https://raw.githubusercontent.com/Microsoft/fhir-server-samples/master/deploy/templates/a zuredeploy-sandbox.json ContentVersion : 1.0.0.0

Parameters : Name Type Value
=============================== ========================= ========== environmentName String xxxx appServicePlanSku String xxxx
aadAuthority String
xxxx aadFhirServerAudience String
aadDashboardClientId String xxxx aadDashboardClientSecret String xxxx aadServiceClientId String xxxx aadServiceClientSecret String xxxx smartAppClientId String xxxx fhirServerTemplateUrl String
https://raw.githubusercontent.com/microsoft/fhir-server/master/samples/templates/default-azuredeploy.json sqlAdminPassword SecureString
fhirDashboardJSTemplateUrl String https://raw.githubusercontent.com/Microsoft/fh ir-server-samples/master/deploy/templates/azuredeploy-fhirdashboard-js.json fhirApiLocation String westus2
fhirVersion String R4
fhirImporterTemplateUrl String https://raw.githubusercontent.com/Microsoft/fh ir-server-samples/master/deploy/templates/azuredeploy-importer.json smartAppTemplateUrl String
fhirDashboardRepositoryUrl String
https://github.com/Microsoft/fhir-server-samples fhirDashboardRepositoryBranch String master
deployDashboardSourceCode Bool True
usePaaS Bool True
accessPolicies Array [ { "objectId": "xxxx" }, { "objectId": "xxxx" }, { "objectId": "xxxx" } ] solutionType String FhirServerSamples enableExport Bool False

Outputs : DeploymentDebugLogLevel :

Warming up site...

Key : fhirServerUrl Value : https://xxxx.azurehealthcareapis.com Name : fhirServerUrl

Key : dashboardUserUpn Value : xxxx Name : dashboardUserUpn

Key : dashboardUserPassword Value : xxxx Name : dashboardUserPassword

# Contributing

This project welcomes contributions and suggestions. Most contributions require you to agree to a Contributor License Agreement (CLA) declaring that you have the right to, and actually do, grant us the rights to use your contribution. For details, visit https://cla.microsoft.com.

When you submit a pull request, a CLA-bot will automatically determine whether you need to provide a CLA and decorate the PR appropriately (e.g., label, comment). Simply follow the instructions provided by the bot. You will only need to do this once across all repos using our CLA.

This project has adopted the Microsoft Open Source Code of Conduct. For more information see the Code of Conduct FAQ or contact [email protected] with any additional questions or comments.

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