├── .gitignore
├── Dockerfile
├── FhirAADUploader
    ├── .gitignore
    ├── FhirAADUploader.csproj
    ├── Program.cs
    └── appsettings.json
├── README.md
├── azuredeploy.json
├── azuredeploy.parameters.json
└── generate_and_upload.sh


/.gitignore:
--------------------------------------------------------------------------------
1 | .vscode/
2 | *.hansen.json


--------------------------------------------------------------------------------
/Dockerfile:
--------------------------------------------------------------------------------
 1 | FROM microsoft/dotnet:2.1-sdk
 2 | 
 3 | WORKDIR /app
 4 | 
 5 | #Installing JAVA and Synthea
 6 | RUN apt-get update && apt-get install -y software-properties-common python3-software-properties
 7 | RUN echo debconf shared/accepted-oracle-license-v1-1 select true | debconf-set-selections
 8 | RUN echo debconf shared/accepted-oracle-license-v1-1 seen true | debconf-set-selections
 9 | RUN echo "deb http://ppa.launchpad.net/webupd8team/java/ubuntu xenial main" | tee /etc/apt/sources.list.d/webupd8team-java.list
10 | RUN echo "deb-src http://ppa.launchpad.net/webupd8team/java/ubuntu xenial main" | tee -a /etc/apt/sources.list.d/webupd8team-java.list
11 | RUN apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys EEA14886
12 | RUN apt-get update
13 | RUN apt-get install -yq openjdk-8-jdk
14 | 
15 | RUN git clone https://github.com/synthetichealth/synthea.git && \
16 |     cd synthea && \
17 |     ./gradlew build check test
18 | 
19 | # copy csproj and restore as distinct layers
20 | COPY FhirAADUploader/*.csproj .
21 | RUN dotnet restore
22 | 
23 | # copy everything else and build app
24 | COPY FhirAADUploader ./
25 | RUN dotnet publish -c release
26 | 
27 | COPY generate_and_upload.sh ./
28 | RUN chmod +x generate_and_upload.sh
29 | ENTRYPOINT ["bash", "-c", "./generate_and_upload.sh"]
30 | 


--------------------------------------------------------------------------------
/FhirAADUploader/.gitignore:
--------------------------------------------------------------------------------
1 | obj/
2 | .vscode/
3 | bin/
4 | out/


--------------------------------------------------------------------------------
/FhirAADUploader/FhirAADUploader.csproj:
--------------------------------------------------------------------------------
 1 | <Project Sdk="Microsoft.NET.Sdk">
 2 | 
 3 |   <PropertyGroup>
 4 |     <OutputType>Exe</OutputType>
 5 |     <TargetFramework>netcoreapp2.1</TargetFramework>
 6 |     <UserSecretsId>6ab5b2dd-3698-4417-bebd-422639bbe5aa</UserSecretsId>
 7 |   </PropertyGroup>
 8 | 
 9 |   <ItemGroup>
10 |     <PackageReference Include="Microsoft.Extensions.Configuration.EnvironmentVariables" Version="2.1.1" />
11 |     <PackageReference Include="Microsoft.Extensions.Configuration.Json" Version="2.1.1" />
12 |     <PackageReference Include="Microsoft.Extensions.Configuration.UserSecrets" Version="2.1.1" />
13 |     <PackageReference Include="Microsoft.IdentityModel.Clients.ActiveDirectory" Version="3.19.8" />
14 |   </ItemGroup>
15 | 
16 | </Project>
17 | 


--------------------------------------------------------------------------------
/FhirAADUploader/Program.cs:
--------------------------------------------------------------------------------
  1 | using System;
  2 | using System.IO;
  3 | using System.Net.Http;
  4 | using System.Text;
  5 | using System.Threading.Tasks;
  6 | using Microsoft.Extensions.Configuration;
  7 | using Microsoft.IdentityModel.Clients.ActiveDirectory;
  8 | using Newtonsoft.Json;
  9 | using Newtonsoft.Json.Linq;
 10 | 
 11 | namespace FhirAADUploader
 12 | {
 13 |     class Program
 14 |     {
 15 |         public static IConfiguration Configuration { get; set; }
 16 |         private static AuthenticationContext authContext = null;
 17 | 
 18 |         static void Main(string[] args)
 19 |         {
 20 |             Task.Run(() => MainAsync(args)).Wait();
 21 |         }
 22 | 
 23 |         static async Task MainAsync(string[] args)
 24 |         {
 25 |             var builder = new ConfigurationBuilder()
 26 |                 .SetBasePath(Directory.GetCurrentDirectory())
 27 |                 .AddJsonFile("appsettings.json")
 28 |                 .AddEnvironmentVariables()
 29 |                 .AddUserSecrets<Program>();
 30 | 
 31 |             Configuration = builder.Build();
 32 | 
 33 | 
 34 |             //Parse some command line arguments
 35 |             if (args.Length != 2)
 36 |             {
 37 |                 PrintUsage();
 38 |                 return;
 39 |             }
 40 | 
 41 |             string fhirResourcePath = Path.GetFullPath(args[0]);
 42 |             string fhirServerUrl = args[1];
 43 | 
 44 |             Console.WriteLine($"FHIR Resource Path  : {fhirResourcePath}");
 45 |             Console.WriteLine($"FHIR Server URL     : {fhirServerUrl}");
 46 |             Console.WriteLine($"Azure AD Authority  : {Configuration["AzureAD_Authority"]}");
 47 |             Console.WriteLine($"Azure AD Client ID  : {Configuration["AzureAD_ClientId"]}");
 48 |             Console.WriteLine($"Azure AD Audience   : {Configuration["AzureAD_Audience"]}");
 49 | 
 50 |             DirectoryInfo dir = new DirectoryInfo(fhirResourcePath);
 51 |             FileInfo[] files = null;
 52 |             try
 53 |             {
 54 |                 files = dir.GetFiles("*.json");
 55 |             }
 56 |             catch (UnauthorizedAccessException e)
 57 |             {
 58 |                 Console.WriteLine(e.Message);
 59 |             }
 60 |             catch (DirectoryNotFoundException e)
 61 |             {
 62 |                 Console.WriteLine(e.Message);
 63 |                 return;
 64 |             }
 65 | 
 66 |             authContext = new AuthenticationContext(Configuration["AzureAD_Authority"]);
 67 |             ClientCredential clientCredential = new ClientCredential(Configuration["AzureAD_ClientId"], Configuration["AzureAD_ClientSecret"]); ;
 68 |             var client = new HttpClient();
 69 |             client.BaseAddress = new Uri(fhirServerUrl);
 70 | 
 71 |             AuthenticationResult authResult = null;
 72 |             try
 73 |             {
 74 |                 authResult = authContext.AcquireTokenAsync(Configuration["AzureAD_Audience"], clientCredential).Result;
 75 |             }
 76 |             catch (Exception ee)
 77 |             {
 78 |                 Console.WriteLine(
 79 |                     String.Format("An error occurred while acquiring a token\nTime: {0}\nError: {1}\n",
 80 |                     DateTime.Now.ToString(),
 81 |                     ee.ToString()));
 82 |                 return;
 83 |             }
 84 | 
 85 |             foreach (FileInfo f in files)
 86 |             {
 87 |                 Console.WriteLine("Processing file: " + f.FullName);
 88 |                 using (StreamReader reader = File.OpenText(f.FullName))
 89 |                 {
 90 |                     JObject o = (JObject)JToken.ReadFrom(new JsonTextReader(reader));
 91 | 
 92 |                     JArray entries = (JArray)o["entry"];
 93 | 
 94 |                     Console.WriteLine("Number of entries: " + entries.Count);
 95 | 
 96 |                     for (int i = 0; i < entries.Count; i++)
 97 |                     {
 98 |                         string entry_json = (((JObject)entries[i])["resource"]).ToString();
 99 |                         string resource_type = (string)(((JObject)entries[i])["resource"]["resourceType"]);
100 |                         string id = (string)(((JObject)entries[i])["resource"]["id"]);
101 | 
102 |                         //Rewrite subject reference
103 |                         if (((JObject)entries[i])["resource"]["subject"] != null) {
104 |                             string subject_reference = (string)(((JObject)entries[i])["resource"]["subject"]["reference"]);
105 |                             if (!String.IsNullOrEmpty(subject_reference)) 
106 |                             {
107 |                                 for (int j = 0; j < entries.Count; j++)
108 |                                 {
109 |                                     if ((string)(((JObject)entries[j])["fullUrl"]) == subject_reference) 
110 |                                     {
111 |                                         subject_reference = (string)(((JObject)entries[j])["resource"]["resourceType"]) + "/" + (string)(((JObject)entries[j])["resource"]["id"]);
112 |                                         break;
113 |                                     }
114 |                                 }
115 |                             }
116 |                             ((JObject)entries[i])["resource"]["subject"]["reference"] = subject_reference;
117 |                             entry_json = (((JObject)entries[i])["resource"]).ToString();
118 |                         }
119 | 
120 |                         if (((JObject)entries[i])["resource"]["context"] != null) 
121 |                         {
122 |                             string context_reference = (string)(((JObject)entries[i])["resource"]["context"]["reference"]);
123 |                             if (!String.IsNullOrEmpty(context_reference)) 
124 |                             {
125 |                                 for (int j = 0; j < entries.Count; j++)
126 |                                 {
127 |                                     if ((string)(((JObject)entries[j])["fullUrl"]) == context_reference) 
128 |                                     {
129 |                                         context_reference = (string)(((JObject)entries[j])["resource"]["resourceType"]) + "/" + (string)(((JObject)entries[j])["resource"]["id"]);
130 |                                         break;
131 |                                     }
132 |                                 }
133 |                             }
134 |                             ((JObject)entries[i])["resource"]["context"]["reference"] = context_reference;
135 |                             entry_json = (((JObject)entries[i])["resource"]).ToString();
136 |                         }
137 | 
138 |                         
139 |                             
140 |                         //If we already have a token, we should get the cached one, otherwise, refresh
141 |                         authResult = authContext.AcquireTokenAsync(Configuration["AzureAD_Audience"], clientCredential).Result;
142 |                         client.DefaultRequestHeaders.Clear();
143 |                         client.DefaultRequestHeaders.Add("Authorization", "Bearer " + authResult.AccessToken);
144 |                         StringContent content = new StringContent(entry_json, Encoding.UTF8, "application/json");
145 | 
146 |                         HttpResponseMessage uploadResult = null;
147 |                         
148 | 
149 |                         if (String.IsNullOrEmpty(id)) 
150 |                         {
151 |                             uploadResult = await client.PostAsync($"/{resource_type}", content);
152 |                         } 
153 |                         else 
154 |                         {
155 |                             uploadResult = await client.PutAsync($"/{resource_type}/{id}", content);
156 |                         }
157 | 
158 |                         if (!uploadResult.IsSuccessStatusCode)
159 |                         {
160 |                             string resultContent = await uploadResult.Content.ReadAsStringAsync();
161 |                             Console.WriteLine(resultContent);
162 |                         }
163 |                     }
164 |                 }
165 |             }
166 |         }
167 | 
168 |         private static void PrintUsage()
169 |         {
170 |             Console.WriteLine("Usage: ");
171 |             Console.WriteLine("   dotnet run <PATH TO FHIR RESOURCES> <FHIR SERVER URL>");
172 |         }
173 |     }
174 | }
175 | 


--------------------------------------------------------------------------------
/FhirAADUploader/appsettings.json:
--------------------------------------------------------------------------------
1 | {
2 |     "AzureAD_Authority": "https://login.microsoftonline.com/TENANT-ID/",
3 |     "AzureAD_ClientId": "ClientAppId",
4 |     "AzureAD_ClientSecret": "SECRET",
5 |     "AzureAD_Audience": "FHIR Server App ID"
6 | }


--------------------------------------------------------------------------------
/README.md:
--------------------------------------------------------------------------------
 1 | Automated Synthea Generator and FHIR Uploader
 2 | ---------------------------------------------
 3 | 
 4 | This repository builds a Docker image with a Synthea patient generator and a FHIR uploader that can be used with FHIR servers using Azure Active Directory as the OAuth2 provider. Specifically, when started, the Docker container will:
 5 | 
 6 | 1. Generate the desired number of patients.
 7 | 2. Authenticate with Azure Active Directory to obtain a token.
 8 | 3. Upload patients to FHIR server.  
 9 | 
10 | The Azure Active Directory authentication and FHIR server upload is handled by the [`FhirAADUploader`](FhirAADUploader) app, which is a .NET Core command line application.
11 | 
12 | To generate 100 patients and upload them to a FHIR server with URL `https://my-fhir-server.com`:
13 | 
14 | ```
15 | docker run --name synthea --rm -t \ 
16 | -e AzureAD_ClientSecret='AAD-CLIENT-SECRET' \ 
17 | -e AzureAD_ClientId='AAD-CLIENT-ID' \ 
18 | -e AzureAD_Authority='https://login.microsoftonline.com/TENANT-ID/' \ 
19 | -e AzureAD_Audience='AAD-FHIR-API-APP-ID' -e NUMBER_OF_PATIENTS='100' \ 
20 | -e FHIR_SERVER_URL='https://my-fhir-server/com/' hansenms/synthegenerator
21 | ```
22 | 
23 | To build your own version of the Docker image:
24 | 
25 | ```
26 | docker build -t yourrepo/yourtagname .
27 | ```
28 | 
29 | You can use an [Azure Container Instance](https://azure.microsoft.com/en-us/services/container-instances/) to generate and upload the patients. To run this image using the Azure CLI:
30 | 
31 | ```bash
32 | az container create --resource-group RgName \ 
33 | --image hansenms/syntheagenerator --name ContainerInstanceName \ 
34 | --cpu 2 --memory 4 --restart-policy Never \ 
35 | -e AzureAD_ClientSecret='CLIENT-SECRET' \ 
36 | AzureAD_ClientId='CLIENT-ID' \ 
37 | AzureAD_Authority='https://login.microsoftonline.com/TENANT-ID/' \ 
38 | AzureAD_Audience='FHIR-SERVER-API-APP' \ 
39 | FHIR_SERVER_URL='https://my-fhir-server.com/' \ 
40 | NUMBER_OF_PATIENTS='100'
41 | ```
42 | 
43 | There is also a template included in this repository, which you can deploy with PowerShell or Azure CLI. Edit the `azuredeploy.parameters.json` to match your setup. 
44 | 
45 | Deploy with PowerShell like this:
46 | 
47 | ```PowerShell
48 | $rg = New-AzureRmResourceGroup -Name RgName -Location eastus
49 | 
50 | New-AzureRmResourceGroupDeployment -Name synthdeploy ` 
51 | -ResourceGroupName $rg.ResourceGroupName ` 
52 | -TemplateFile .\azuredeploy.json ` 
53 | -TemplateParameterFile .\azuredeploy.parameters.json 
54 | ```
55 | 
56 | Or you can deploy with the Azure CLI:
57 | 
58 | ```bash
59 | #Create a resource group:
60 | RGNAME=MyResourceGroup
61 | az group create --name ${RGNAME} --location eastus
62 | 
63 | #Deploy using the template
64 | az group deployment create --resource-group ${RGNAME} \ 
65 | --template-file ./azuredeploy.json \ 
66 | --parameters @azuredeploy.parameters.json
67 | ```
68 | 
69 | You can also deploy through the portal. Simply hit the button below and fill in the details:
70 | 
71 | <a href="https://transmogrify.azurewebsites.net/azuredeploy.json" target="_blank">
72 |     <img src="http://azuredeploy.net/deploybutton.png"/>
73 | </a>
74 | 


--------------------------------------------------------------------------------
/azuredeploy.json:
--------------------------------------------------------------------------------
  1 | {
  2 |     "$schema": "https://schema.management.azure.com/schemas/2015-01-01/deploymentTemplate.json#",
  3 |     "contentVersion": "1.0.0.0",
  4 |     "parameters": {
  5 |         "Authority": {
  6 |             "type": "string",
  7 |             "metadata": {
  8 |                 "description": "Azure Active Directory Authority"
  9 |             },
 10 |             "defaultValue": "https://login.microsoftonline.com/microsoft.onmicrosoft.com/"
 11 |         },
 12 |         "ClientId": {
 13 |             "type": "string",
 14 |             "metadata": {
 15 |                 "description": "Azure Active Directory Client Id"
 16 |             }
 17 |         },
 18 |         "ClientSecret": {
 19 |             "type": "string",
 20 |             "metadata": {
 21 |                 "description": "Azure Active Directory Client Secret"
 22 |             }
 23 |         },
 24 |         "Audience": {
 25 |             "type": "string",
 26 |             "metadata": {
 27 |                 "description": "Azure Active Directory FHIR API App (ID or URI)"
 28 |             }
 29 |         },
 30 |         "NumberOfPatients": {
 31 |             "type": "int",
 32 |             "metadata": {
 33 |                 "description": "Number of Patients to Generate"
 34 |             },
 35 |             "defaultValue": 100
 36 |         },
 37 |         "AdditionalSyntheaArgs": {
 38 |             "type": "string",
 39 |             "defaultValue": "",
 40 |             "metadata": {
 41 |                 "description": "Additional Syntea args, e.g., '-a 0-18'"
 42 |             }
 43 |         },
 44 |         "FhirServerUrl": {
 45 |             "type": "string",
 46 |             "metadata": {
 47 |                 "description": "FHIR Server URL"
 48 |             }
 49 |         },
 50 |         "DockerImage": {
 51 |             "type": "string",
 52 |             "metadata": {
 53 |                 "description": "Name of Docker Image"
 54 |             },
 55 |             "defaultValue": "hansenms/syntheagenerator:latest"
 56 |         }
 57 |     },
 58 |     "resources": [
 59 |         {
 60 |             "name": "SyntheaGenerator",
 61 |             "type": "Microsoft.ContainerInstance/containerGroups",
 62 |             "apiVersion": "2018-02-01-preview",
 63 |             "location": "[resourceGroup().location]",
 64 |             "properties": {
 65 |                 "containers": [
 66 |                     {
 67 |                         "name": "syntheagenerator",
 68 |                         "properties": {
 69 |                             "image": "[parameters('DockerImage')]",
 70 |                             "command": [
 71 |                                 "bash", "-c", "./generate_and_upload.sh"
 72 |                             ],
 73 |                             "environmentVariables": [
 74 |                                 {
 75 |                                     "name": "AzureAD_ClientId",
 76 |                                     "value": "[parameters('ClientId')]"
 77 |                                 },
 78 |                                 {
 79 |                                     "name": "AzureAD_ClientSecret",
 80 |                                     "value": "[parameters('ClientSecret')]"
 81 |                                 },
 82 |                                 {
 83 |                                     "name": "AzureAD_Audience",
 84 |                                     "value": "[parameters('Audience')]"
 85 |                                 },
 86 |                                 {
 87 |                                     "name": "AzureAD_Authority",
 88 |                                     "value": "[parameters('Authority')]"
 89 |                                 },
 90 |                                 {
 91 |                                     "name": "NUMBER_OF_PATIENTS",
 92 |                                     "value": "[parameters('NumberOfPatients')]"
 93 |                                 },
 94 |                                 {
 95 |                                     "name": "ADDITIONAL_SYNTHEA_ARGS",
 96 |                                     "value": "[parameters('AdditionalSyntheaArgs')]"
 97 |                                 },
 98 |                                 {
 99 |                                     "name": "FHIR_SERVER_URL",
100 |                                     "value": "[parameters('FhirServerUrl')]"
101 |                                 }
102 |                             ],
103 |                             "resources": {
104 |                                 "requests": {
105 |                                     "cpu": 2,
106 |                                     "memoryInGB": 4
107 |                                 }
108 |                             }
109 |                         }
110 |                     }
111 |                 ],
112 |                 "restartPolicy": "OnFailure",
113 |                 "osType": "Linux"
114 |             }
115 |         }
116 |     ]
117 | }


--------------------------------------------------------------------------------
/azuredeploy.parameters.json:
--------------------------------------------------------------------------------
 1 | {
 2 |     "Authority":  {
 3 |         "value":  "https://login.microsoftonline.com/microsoft.onmicrosoft.com/"
 4 |     },
 5 |     "ClientId":  {
 6 |         "value":  "CLIENT-ID"
 7 |     },
 8 |     "ClientSecret":  {
 9 |         "value":  "CLIENT-SECRET"
10 |     },
11 |     "Audience":  {
12 |         "value":  "https://my-fhir-server.com"
13 |     },
14 |     "NumberOfPatients":  {
15 |         "value":  100
16 |     },
17 |     "FhirServerUrl":  {
18 |         "value":  "https://my-fhir-server.com/"
19 |     }
20 | }


--------------------------------------------------------------------------------
/generate_and_upload.sh:
--------------------------------------------------------------------------------
1 | #!/bin/bash
2 | 
3 | cd /app/synthea
4 | ./run_synthea -p $NUMBER_OF_PATIENTS $ADDITIONAL_SYNTHEA_ARGS
5 | 
6 | cd /app
7 | dotnet run /app/synthea/output/fhir $FHIR_SERVER_URL
8 | 
9 | 


--------------------------------------------------------------------------------