Updated FhirClient (#167)

* removed hl7 fhir client and leveraging health team client * changed to local.appsettings.json * removed FhirOperationException * removed r4 common test proj and made other updates * updated nuget package sources * moved ServiceCollectionExtensions to Microsoft.Health.Extensions.Fhir project * removed unnecessary package references * added service collection extension and updated fhirservice validtor * updated BearerTokenAuthMessageHandler * updating inputs on .net core sdk task * updated r4 params to base constructor * removed updates to ResourceIdentityServiceFactory * updated ResolveResourceIdentityService * refactored repo to service, implemeneted retry and timeout policies on httpclient, updated fhirexceptionprocessor * added fhirclient validation * fix fhirclientvalidator tests * Updated AddFhirClient and corresponding tests * removed identifierextensions and updated validation * added ToSearchQueryParameter to SearchExtensions * added null check for logger in addfhirclient Co-authored-by: Mackenzie Dolishny <[email protected]>
microsoft · Feb 16, 2022 · 726cf7d · 726cf7d
1 parent 82f3b26
commit 726cf7d
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Showing 43 changed files with 735 additions and 550 deletions.
diff --git a/build/build.yml b/build/build.yml
@@ -7,6 +7,8 @@ steps:
   displayName: 'Use .NET Core sdk 6.0.x'
   inputs:
     version: 6.0.x
+    selectOrConfig: configs
+    nugetConfigPath: nuget.config
 
 - script: dotnet build --configuration $(buildConfiguration) --version-suffix $(build.buildNumber) /warnaserror
   displayName: 'dotnet build $(buildConfiguration)'

diff --git a/nuget.config b/nuget.config
@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="utf-8"?>
+<configuration>
+	<config>
+		<add key="repositoryPath" value="packages" />
+	</config>
+	<packageSources>
+		<!-- When <clear /> is present, previously defined sources are ignored -->
+		<clear />
+		<add key="nuget.org" value="https://api.nuget.org/v3/index.json" />
+		<add key="Microsoft Health OSS" value="https://microsofthealthoss.pkgs.visualstudio.com/FhirServer/_packaging/Public/nuget/v3/index.json" />
+	</packageSources>
+	<activePackageSource>
+		<add key="All" value="(Aggregate source)" />
+	</activePackageSource>
+	<disabledPackageSources>
+		<add key="Microsoft Visual Studio Offline Packages" value="true" />
+	</disabledPackageSources>
+</configuration>
diff --git a/src/console/MeasurementCollectionToFhir/ProcessorStartup.cs b/src/console/MeasurementCollectionToFhir/ProcessorStartup.cs
@@ -1,6 +1,5 @@
 using EnsureThat;
 using Hl7.Fhir.Model;
-using Hl7.Fhir.Rest;
 using Microsoft.Extensions.Caching.Memory;
 using Microsoft.Extensions.Configuration;
 using Microsoft.Extensions.DependencyInjection;
@@ -10,6 +9,7 @@
 using Microsoft.Health.Common;
 using Microsoft.Health.Extensions.Fhir;
 using Microsoft.Health.Extensions.Fhir.Config;
+using Microsoft.Health.Extensions.Fhir.Service;
 using Microsoft.Health.Fhir.Ingest.Config;
 using Microsoft.Health.Fhir.Ingest.Host;
 using Microsoft.Health.Fhir.Ingest.Service;
@@ -38,13 +38,15 @@ public void ConfigureServices(IServiceCollection services)
             services.Configure<ResourceIdentityOptions>(Configuration.GetSection("ResourceIdentity"));
             services.Configure<FhirClientFactoryOptions>(Configuration.GetSection("FhirClient"));
 
-            services.TryAddSingleton<IFactory<FhirClient>, FhirClientFactory>();
-            services.TryAddSingleton(sp => sp.GetRequiredService<IFactory<FhirClient>>().Create());
-            services.TryAddSingleton<IFhirTemplateProcessor<ILookupTemplate<IFhirTemplate>, Observation>, R4FhirLookupTemplateProcessor>();
+            services.AddFhirClient(Configuration);
             services.TryAddSingleton(ResolveResourceIdentityService);
+            services.TryAddSingleton<IFhirService, FhirService>();
+
+            services.TryAddSingleton<IFhirTemplateProcessor<ILookupTemplate<IFhirTemplate>, Observation>, R4FhirLookupTemplateProcessor>();
             services.TryAddSingleton<IMemoryCache>(sp => new MemoryCache(Options.Create(new MemoryCacheOptions { SizeLimit = 5000 })));
             services.TryAddSingleton<FhirImportService, R4FhirImportService>();
 
+            services.TryAddSingleton<ResourceManagementService>();
             services.TryAddSingleton<MeasurementFhirImportOptions>();
             services.TryAddSingleton<MeasurementFhirImportService>();
             services.TryAddSingleton(ResolveMeasurementImportProvider);
@@ -65,9 +67,9 @@ private static IResourceIdentityService ResolveResourceIdentityService(IServiceP
         {
             EnsureArg.IsNotNull(serviceProvider, nameof(serviceProvider));
 
-            var fhirClient = serviceProvider.GetRequiredService<FhirClient>();
+            var fhirService = serviceProvider.GetRequiredService<IFhirService>();
             var resourceIdentityOptions = serviceProvider.GetRequiredService<IOptions<ResourceIdentityOptions>>();
-            return ResourceIdentityServiceFactory.Instance.Create(resourceIdentityOptions.Value, fhirClient);
+            return ResourceIdentityServiceFactory.Instance.Create(resourceIdentityOptions.Value, fhirService);
         }
     }
 }
diff --git a/src/console/Microsoft.Health.Fhir.Ingest.Console.csproj b/src/console/Microsoft.Health.Fhir.Ingest.Console.csproj
@@ -20,6 +20,7 @@
 		<ProjectReference Include="..\lib\Microsoft.Health.Fhir.Ingest\Microsoft.Health.Fhir.Ingest.csproj" />
 		<ProjectReference Include="..\lib\Microsoft.Health.Fhir.R4.Ingest\Microsoft.Health.Fhir.R4.Ingest.csproj" />
 		<ProjectReference Include="..\lib\Microsoft.Health.Expressions\Microsoft.Health.Expressions.csproj" />
+		<PackageReference Include="Microsoft.Health.Fhir.R4.Client" Version="2.0.55" />
 	</ItemGroup>
 
 	<ItemGroup>

diff --git a/src/func/Microsoft.Health.Fhir.Ingest.Host/Microsoft.Health.Fhir.Ingest.Host.csproj b/src/func/Microsoft.Health.Fhir.Ingest.Host/Microsoft.Health.Fhir.Ingest.Host.csproj
@@ -35,7 +35,7 @@
       <IncludeAssets>runtime; build; native; contentfiles; analyzers; buildtransitive</IncludeAssets>
     </PackageReference>
     <PackageReference Include="Microsoft.NET.Sdk.Functions" Version="4.0.1" />
-    <PackageReference Include="Ensure.That" Version="10.0.0" />
+    <PackageReference Include="Ensure.That" Version="10.1.0" />
     <PackageReference Include="StyleCop.Analyzers" Version="1.1.118">
       <PrivateAssets>all</PrivateAssets>
       <IncludeAssets>runtime; build; native; contentfiles; analyzers; buildtransitive</IncludeAssets>

diff --git a/src/lib/Microsoft.Health.Extensions.Fhir.R4/BearerTokenAuthorizationMessageHandler.cs b/src/lib/Microsoft.Health.Extensions.Fhir.R4/BearerTokenAuthorizationMessageHandler.cs
@@ -0,0 +1,54 @@
+// -------------------------------------------------------------------------------------------------
+// Copyright (c) Microsoft Corporation. All rights reserved.
+// Licensed under the MIT License (MIT). See LICENSE in the repo root for license information.
+// -------------------------------------------------------------------------------------------------
+
+using System;
+using System.Net.Http;
+using System.Net.Http.Headers;
+using System.Threading;
+using System.Threading.Tasks;
+using Azure.Core;
+using EnsureThat;
+using Microsoft.Health.Common.Telemetry;
+using Microsoft.Health.Extensions.Fhir.Telemetry.Metrics;
+using Microsoft.Health.Logging.Telemetry;
+
+namespace Microsoft.Health.Extensions.Fhir
+{
+    public class BearerTokenAuthorizationMessageHandler : DelegatingHandler
+    {
+        public BearerTokenAuthorizationMessageHandler(Uri uri, TokenCredential tokenCredentialProvider, ITelemetryLogger logger)
+        {
+            TokenCredential = EnsureArg.IsNotNull(tokenCredentialProvider, nameof(tokenCredentialProvider));
+            Uri = EnsureArg.IsNotNull(uri, nameof(uri));
+            Logger = EnsureArg.IsNotNull(logger, nameof(logger));
+            Scopes = new string[] { Uri.ToString().EndsWith(@"/") ? Uri + ".default" : Uri + "/.default" };
+        }
+
+        private ITelemetryLogger Logger { get; }
+
+        private TokenCredential TokenCredential { get; }
+
+        private Uri Uri { get; }
+
+        private string[] Scopes { get; }
+
+        protected override async Task<HttpResponseMessage> SendAsync(HttpRequestMessage request, CancellationToken cancellationToken)
+        {
+            var requestContext = new TokenRequestContext(Scopes);
+            var accessToken = await TokenCredential.GetTokenAsync(requestContext, cancellationToken);
+            request.Headers.Authorization = new AuthenticationHeaderValue("Bearer", accessToken.Token);
+            var response = await base.SendAsync(request, cancellationToken);
+
+            if (!response.IsSuccessStatusCode)
+            {
+                var statusDescription = response.ReasonPhrase.Replace(" ", string.Empty);
+                var severity = response.StatusCode == System.Net.HttpStatusCode.TooManyRequests ? ErrorSeverity.Informational : ErrorSeverity.Critical;
+                Logger.LogMetric(FhirClientMetrics.HandledException($"{ErrorType.FHIRServiceError}{statusDescription}", severity), 1);
+            }
+
+            return response;
+        }
+    }
+}
diff --git a/src/lib/Microsoft.Health.Extensions.Fhir.R4/BundleExtensions.cs b/src/lib/Microsoft.Health.Extensions.Fhir.R4/BundleExtensions.cs
@@ -9,7 +9,7 @@
 using System.Threading.Tasks;
 using EnsureThat;
 using Hl7.Fhir.Model;
-using Hl7.Fhir.Rest;
+using Microsoft.Health.Extensions.Fhir.Service;
 
 namespace Microsoft.Health.Extensions.Fhir
 {
@@ -41,15 +41,18 @@ public static IEnumerable<TResource> ReadFromBundle<TResource>(this Bundle bundl
             }
         }
 
-        public static async Task<TResource> ReadOneFromBundleWithContinuationAsync<TResource>(this Bundle bundle, FhirClient fhirClient, bool throwOnMultipleFound = true)
+        public static async Task<TResource> ReadOneFromBundleWithContinuationAsync<TResource>(
+            this Bundle bundle,
+            IFhirService fhirService,
+            bool throwOnMultipleFound = true)
             where TResource : Resource, new()
         {
             if (bundle == null)
             {
                 return null;
             }
 
-            var resources = await bundle?.ReadFromBundleWithContinuationAsync<TResource>(fhirClient, 2);
+            var resources = await bundle?.ReadFromBundleWithContinuationAsync<TResource>(fhirService, 2);
 
             var resourceCount = resources.Count();
             if (resourceCount == 0)
@@ -75,13 +78,17 @@ public static int EntryCount(this Bundle bundle)
             return bundle?.Entry?.Count ?? 0;
         }
 
-        public static async Task<IEnumerable<TResource>> ReadFromBundleWithContinuationAsync<TResource>(this Bundle bundle, FhirClient fhirClient, int? count = null)
+        private static async Task<IEnumerable<TResource>> ReadFromBundleWithContinuationAsync<TResource>(
+            this Bundle bundle,
+            IFhirService fhirService,
+            int? count = null)
             where TResource : Resource
         {
-            EnsureArg.IsNotNull(fhirClient, nameof(fhirClient));
+            EnsureArg.IsNotNull(fhirService, nameof(fhirService));
 
             var resources = new List<TResource>();
-            while (bundle != null)
+
+            Action<Bundle> storeResources = (bundle) =>
             {
                 foreach (var r in bundle.ReadFromBundle<TResource>(count))
                 {
@@ -96,30 +103,16 @@ public static async Task<IEnumerable<TResource>> ReadFromBundleWithContinuationA
                         count--;
                     }
                 }
+            };
+
+            storeResources.Invoke(bundle);
 
-                bundle = await fhirClient.ContinueAsync(bundle).ConfigureAwait(false);
+            await foreach (var currentBundle in fhirService.IterateOverAdditionalBundlesAsync(bundle))
+            {
+                storeResources.Invoke(currentBundle);
             }
 
             return resources;
         }
-
-        public static async Task<IEnumerable<TResource>> SearchWithContinuationAsync<TResource>(this FhirClient fhirClient, SearchParams searchParams)
-            where TResource : Resource
-        {
-            EnsureArg.IsNotNull(fhirClient, nameof(fhirClient));
-            EnsureArg.IsNotNull(searchParams, nameof(searchParams));
-
-            var result = await fhirClient.SearchAsync<TResource>(searchParams).ConfigureAwait(false);
-            return await result.ReadFromBundleWithContinuationAsync<TResource>(fhirClient, searchParams.Count).ConfigureAwait(false);
-        }
-
-        public static async Task<IEnumerable<TResource>> GetWithContinuationAsync<TResource>(this FhirClient fhirClient, Uri resourceUri, int? count = null)
-            where TResource : Resource
-        {
-            EnsureArg.IsNotNull(fhirClient, nameof(fhirClient));
-
-            var result = await fhirClient.GetAsync(resourceUri).ConfigureAwait(false) as Bundle;
-            return await result.ReadFromBundleWithContinuationAsync<TResource>(fhirClient, count).ConfigureAwait(false);
-        }
     }
 }
diff --git a/src/lib/Microsoft.Health.Extensions.Fhir.R4/FhirClientFactory.cs b/src/lib/Microsoft.Health.Extensions.Fhir.R4/FhirClientFactory.cs