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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:
<center><img src="images//fhir-server-samples-paas.png" width="512"></center>Or the open source FHIR Server for Azure:
<center><img src="images//fhir-server-samples-oss.png" width="512"></center>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
$exportyou 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:
$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:
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 <AAD 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 <ENVIRONMENTNAME> -UsePaaS $false
or the managed Azure API for FHIR:
.\Create-FhirServerSamplesEnvironment.ps1 -EnvironmentName <ENVIRONMENTNAME> -UsePaaS $true
and to enable $export:
.\Create-FhirServerSamplesEnvironment.ps1 -EnvironmentName <ENVIRONMENTNAME> -UsePaaS $true -EnableExport $true
To delete the senario:
.\Delete-FhirServerSamplesEnvironment.ps1 -EnvironmentName <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 <ENVIRONMENTNAME> -UsePaaS <TRUE/FALSE> -AdminPassword $(ConvertTo-SecureString -AsPlainText -Force "<YOURPASSWORD>")
If the deployment is successful, you would see information like below being written on your terminal or CloudShell as the scripts run:
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 opencode@microsoft.com with any additional questions or comments.