Merge branch 'master' into personal/poadhikari/negative_tests_added

microsoft · Dec 13, 2018 · aa7443e · aa7443e
2 parents b163532 + 090e818
commit aa7443e
Show file tree

Hide file tree

Showing 44 changed files with 615 additions and 1,152 deletions.
diff --git a/Directory.Build.props b/Directory.Build.props
@@ -0,0 +1,16 @@
+<Project>
+    <PropertyGroup>
+        <TreatWarningsAsErrors>true</TreatWarningsAsErrors>
+        <WarningsAsErrors />
+        <DebugType>Full</DebugType>
+        <LangVersion>7.3</LangVersion>
+        <HighEntropyVA>true</HighEntropyVA>
+        <EnableSourceLink Condition="$([MSBuild]::IsOSPlatform('osx'))">false</EnableSourceLink>
+        <EnableSourceControlManagerQueries>$(EnableSourceLink)</EnableSourceControlManagerQueries>
+    </PropertyGroup>
+    <PropertyGroup Condition=" '$(EnableSourceLink)' == 'true' ">
+        <PublishRepositoryUrl>true</PublishRepositoryUrl>
+        <EmbedUntrackedSources>true</EmbedUntrackedSources>
+        <AllowedOutputExtensionsInPackageBuildOutputFolder>$(AllowedOutputExtensionsInPackageBuildOutputFolder);.pdb</AllowedOutputExtensionsInPackageBuildOutputFolder>
+    </PropertyGroup>
+</Project>
diff --git a/docs/Roadmap.md b/docs/Roadmap.md
@@ -56,8 +56,14 @@ Extensions are not yet supported. Documents with extensions will get stored and
 ## Profiling
 Profiling is not supported yet, but the project aims to support storing profiles and validating against stored profiles.
 
+## Batch/Transaction
+Currently there is no support for batch/transaction (https://www.hl7.org/fhir/http.html#transaction). This is something we are investigating and expect to support in future releases.
+
+## Conditional operations
+Conditional operations (update, delete, create) are currently not supported. This partially ties to supporting transactions. Our roadmap includes support for conditional operations.
+
 ## FHIR Versions
 The FHIR Server currently supports FHIR 3.0.1 but the intention is to support multiple versions in the future.
 
 ## Azure Data Factory Connector
-Users of the Microsoft FHIR Server will want to use analytics and machine learning tools in Azure to gain insights from the data stored in the FHIR Server. [Azure Data Factory](https://azure.microsoft.com/en-us/services/data-factory/) is the natural choice for facilitating the export and transformation of data for downstream analytics. See an [example of using Data Factory with the Microsoft FHIR Server](https://github.com/hansenms/FhirDemo). This example was based on accessing the data in the FHIR Server directly through the FHIR API. One of the Microsoft FHIR Server for Azure project's goals is to provide a more direct and efficient integration with Data Factory. Specifically, the goal is to provide a first class connector to allow the FHIR Server to serve as source and sink for Data Factory.  
+Users of the Microsoft FHIR Server will want to use analytics and machine learning tools in Azure to gain insights from the data stored in the FHIR Server. [Azure Data Factory](https://azure.microsoft.com/en-us/services/data-factory/) is the natural choice for facilitating the export and transformation of data for downstream analytics. See an [example of using Data Factory with the Microsoft FHIR Server](https://github.com/hansenms/FhirDemo). This example was based on accessing the data in the FHIR Server directly through the FHIR API. One of the Microsoft FHIR Server for Azure project's goals is to provide a more direct and efficient integration with Data Factory. Specifically, the goal is to provide a first class connector to allow the FHIR Server to serve as source and sink for Data Factory.  
diff --git a/...lth.Extensions.DependencyInjection/Microsoft.Health.Extensions.DependencyInjection.csproj b/...lth.Extensions.DependencyInjection/Microsoft.Health.Extensions.DependencyInjection.csproj
@@ -3,14 +3,6 @@
   <PropertyGroup>
     <TargetFramework>netstandard2.0</TargetFramework>
     <CodeAnalysisRuleSet>..\..\CustomAnalysisRules.ruleset</CodeAnalysisRuleSet>
-    <TreatWarningsAsErrors>true</TreatWarningsAsErrors>
-    <WarningsAsErrors />
-    <DebugType>Full</DebugType>
-    <LangVersion>latest</LangVersion>
-    <HighEntropyVA>true</HighEntropyVA>
-    <PublishRepositoryUrl>true</PublishRepositoryUrl>
-    <EmbedUntrackedSources>true</EmbedUntrackedSources>
-    <AllowedOutputExtensionsInPackageBuildOutputFolder>$(AllowedOutputExtensionsInPackageBuildOutputFolder);.pdb</AllowedOutputExtensionsInPackageBuildOutputFolder>
   </PropertyGroup>
 
   <ItemGroup>

diff --git a/src/Microsoft.Health.Fhir.Api.UnitTests/Features/Headers/FhirHeadersTests.cs b/src/Microsoft.Health.Fhir.Api.UnitTests/Features/Headers/FhirHeadersTests.cs
@@ -8,6 +8,7 @@
 using Hl7.Fhir.Model;
 using Microsoft.Health.Fhir.Api.Features.ActionResults;
 using Microsoft.Health.Fhir.Api.Features.Headers;
+using Microsoft.Health.Fhir.Core.Features.Persistence;
 using Microsoft.Health.Fhir.Core.Features.Routing;
 using Microsoft.Net.Http.Headers;
 using NSubstitute;
@@ -91,9 +92,9 @@ public void WhenAddingSameHeaderTwice_ThenOnlyOneHeaderIsPresent()
         [Fact]
         public void WhenAddingStringEtag_ThenStringETagIsReturned()
         {
-            var fhirResult = FhirResult.Create(_mockResource).SetETagHeader("etag");
+            var fhirResult = FhirResult.Create(_mockResource).SetETagHeader(WeakETag.FromVersionId("etag"));
 
-            Assert.Equal("etag", fhirResult.Headers[HeaderNames.ETag]);
+            Assert.Equal("W/\"etag\"", fhirResult.Headers[HeaderNames.ETag]);
         }
     }
 }
diff --git a/src/Microsoft.Health.Fhir.Api/Controllers/FhirController.cs b/src/Microsoft.Health.Fhir.Api/Controllers/FhirController.cs
@@ -12,7 +12,6 @@
 using Hl7.Fhir.Model;
 using MediatR;
 using Microsoft.AspNetCore.Authorization;
-using Microsoft.AspNetCore.Http;
 using Microsoft.AspNetCore.Mvc;
 using Microsoft.Extensions.Logging;
 using Microsoft.Extensions.Options;
@@ -24,15 +23,12 @@
 using Microsoft.Health.Fhir.Api.Features.Headers;
 using Microsoft.Health.Fhir.Api.Features.Routing;
 using Microsoft.Health.Fhir.Api.Features.Security;
+using Microsoft.Health.Fhir.Core.Extensions;
 using Microsoft.Health.Fhir.Core.Features;
 using Microsoft.Health.Fhir.Core.Features.Context;
 using Microsoft.Health.Fhir.Core.Features.Persistence;
 using Microsoft.Health.Fhir.Core.Features.Routing;
-using Microsoft.Health.Fhir.Core.Messages.Create;
-using Microsoft.Health.Fhir.Core.Messages.Delete;
-using Microsoft.Health.Fhir.Core.Messages.Get;
 using Microsoft.Health.Fhir.Core.Messages.Search;
-using Microsoft.Health.Fhir.Core.Messages.Upsert;
 using Microsoft.Health.Fhir.Core.Models;
 using Microsoft.Health.Fhir.ValueSets;
 using Microsoft.Net.Http.Headers;
@@ -149,8 +145,9 @@ public IActionResult CustomError(int? statusCode = null)
         [Authorize(PolicyNames.WritePolicy)]
         public async Task<IActionResult> Create([FromBody] Resource resource)
         {
-            var response = await _mediator.Send<UpsertResourceResponse>(new CreateResourceRequest(resource), HttpContext.RequestAborted);
-            return FhirResult.Create(response.Outcome.Resource, HttpStatusCode.Created)
+            Resource response = await _mediator.CreateResourceAsync(resource, HttpContext.RequestAborted);
+
+            return FhirResult.Create(response, HttpStatusCode.Created)
                 .SetETagHeader()
                 .SetLastModifiedHeader()
                 .SetLocationHeader(_urlResolver);
@@ -175,21 +172,22 @@ public async Task<IActionResult> Update([FromBody] Resource resource)
                 weakETag = WeakETag.FromWeakETag(suppliedWeakETag);
             }
 
-            var response = await _mediator.Send<UpsertResourceResponse>(new UpsertResourceRequest(resource, weakETag), HttpContext.RequestAborted);
-            switch (response.Outcome.Outcome)
+            SaveOutcome response = await _mediator.UpsertResourceAsync(resource, weakETag, HttpContext.RequestAborted);
+
+            switch (response.Outcome)
             {
                 case SaveOutcomeType.Created:
-                    return FhirResult.Create(response.Outcome.Resource, HttpStatusCode.Created)
+                    return FhirResult.Create(response.Resource, HttpStatusCode.Created)
                         .SetETagHeader()
                         .SetLastModifiedHeader()
                         .SetLocationHeader(_urlResolver);
                 case SaveOutcomeType.Updated:
-                    return FhirResult.Create(response.Outcome.Resource, HttpStatusCode.OK)
+                    return FhirResult.Create(response.Resource, HttpStatusCode.OK)
                         .SetETagHeader()
                         .SetLastModifiedHeader();
             }
 
-            return FhirResult.Create(response.Outcome.Resource, HttpStatusCode.BadRequest);
+            return FhirResult.Create(response.Resource, HttpStatusCode.BadRequest);
         }
 
         /// <summary>
@@ -203,8 +201,9 @@ public async Task<IActionResult> Update([FromBody] Resource resource)
         [Authorize(PolicyNames.ReadPolicy)]
         public async Task<IActionResult> Read(string type, string id)
         {
-            var response = await _mediator.Send(new GetResourceRequest(type, id), HttpContext.RequestAborted);
-            return FhirResult.Create(response.Resource)
+            Resource response = await _mediator.GetResourceAsync(new ResourceKey(type, id), HttpContext.RequestAborted);
+
+            return FhirResult.Create(response)
                 .SetETagHeader()
                 .SetLastModifiedHeader();
         }
@@ -226,9 +225,9 @@ public async Task<IActionResult> SystemHistory(
             [FromQuery(Name = KnownQueryParameterNames.Count)] int? count,
             string ct)
         {
-            var response = await _mediator.Send(new SearchResourceHistoryRequest(since, at, count, ct), HttpContext.RequestAborted);
+            Bundle response = await _mediator.SearchResourceHistoryAsync(since, at, count, ct, HttpContext.RequestAborted);
 
-            return FhirResult.Create(response.Bundle);
+            return FhirResult.Create(response);
         }
 
         /// <summary>
@@ -250,9 +249,9 @@ public async Task<IActionResult> TypeHistory(
             [FromQuery(Name = KnownQueryParameterNames.Count)] int? count,
             string ct)
         {
-            var response = await _mediator.Send(new SearchResourceHistoryRequest(type, since, at, count, ct), HttpContext.RequestAborted);
+            Bundle response = await _mediator.SearchResourceHistoryAsync(type, since, at, count, ct, HttpContext.RequestAborted);
 
-            return FhirResult.Create(response.Bundle);
+            return FhirResult.Create(response);
         }
 
         /// <summary>
@@ -276,9 +275,9 @@ public async Task<IActionResult> History(
             [FromQuery(Name = KnownQueryParameterNames.Count)] int? count,
             string ct)
         {
-            var response = await _mediator.Send(new SearchResourceHistoryRequest(type, id, since, at, count, ct), HttpContext.RequestAborted);
+            Bundle response = await _mediator.SearchResourceHistoryAsync(type, id, since, at, count, ct, HttpContext.RequestAborted);
 
-            return FhirResult.Create(response.Bundle);
+            return FhirResult.Create(response);
         }
 
         /// <summary>
@@ -293,8 +292,9 @@ public async Task<IActionResult> History(
         [Authorize(PolicyNames.ReadPolicy)]
         public async Task<IActionResult> VRead(string type, string id, string vid)
         {
-            var response = await _mediator.Send(new GetResourceRequest(type, id, vid), HttpContext.RequestAborted);
-            return FhirResult.Create(response.Resource, HttpStatusCode.OK)
+            var response = await _mediator.GetResourceAsync(new ResourceKey(type, id, vid), HttpContext.RequestAborted);
+
+            return FhirResult.Create(response, HttpStatusCode.OK)
                     .SetETagHeader()
                     .SetLastModifiedHeader();
         }
@@ -322,7 +322,7 @@ public async Task<IActionResult> Delete(string type, string id, [FromQuery]bool
                 return Forbid();
             }
 
-            DeleteResourceResponse response = await _mediator.Send(new DeleteResourceRequest(type, id, hardDelete), HttpContext.RequestAborted);
+            var response = await _mediator.DeleteResourceAsync(new ResourceKey(type, id), hardDelete, HttpContext.RequestAborted);
 
             return FhirResult.NoContent().SetETagHeader(response.WeakETag);
         }
@@ -425,16 +425,16 @@ public async Task<IActionResult> SearchCompartmentByResourceType(string compartm
 
         private async Task<IActionResult> PerformCompartmentSearch(string compartmentType, string compartmentId, string resourceType, IReadOnlyList<Tuple<string, string>> queries)
         {
-            var response = await _mediator.Send(new CompartmentResourceRequest(compartmentType, compartmentId, resourceType, queries), HttpContext.RequestAborted);
+            Bundle response = await _mediator.SearchResourceCompartmentAsync(compartmentType, compartmentId, resourceType, queries, HttpContext.RequestAborted);
 
-            return FhirResult.Create(response.Bundle);
+            return FhirResult.Create(response);
         }
 
         private async Task<IActionResult> PerformSearch(string type, IReadOnlyList<Tuple<string, string>> queries)
         {
-            var response = await _mediator.Send(new SearchResourceRequest(type, queries), HttpContext.RequestAborted);
+            Bundle response = await _mediator.SearchResourceAsync(type, queries, HttpContext.RequestAborted);
 
-            return FhirResult.Create(response.Bundle);
+            return FhirResult.Create(response);
         }
 
         /// <summary>
@@ -447,14 +447,9 @@ private async Task<IActionResult> PerformSearch(string type, IReadOnlyList<Tuple
         [Route(KnownRoutes.Metadata, Name = RouteNames.Metadata)]
         public async Task<IActionResult> Metadata(bool system = false)
         {
-            if (system)
-            {
-                var sysResponse = await _mediator.Send(new GetSystemCapabilitiesRequest(), HttpContext.RequestAborted);
-                return FhirResult.Create(sysResponse.CapabilityStatement);
-            }
+            CapabilityStatement response = await _mediator.GetCapabilitiesAsync(system, HttpContext.RequestAborted);
 
-            var response = await _mediator.Send(new GetCapabilitiesRequest(), HttpContext.RequestAborted);
-            return FhirResult.Create(response.CapabilityStatement);
+            return FhirResult.Create(response);
         }
     }
 }
diff --git a/src/Microsoft.Health.Fhir.Api/Features/Headers/FhirHeaders.cs b/src/Microsoft.Health.Fhir.Api/Features/Headers/FhirHeaders.cs
@@ -50,16 +50,6 @@ public static FhirResult SetETagHeader(this FhirResult fhirResult, WeakETag weak
             return fhirResult;
         }
 
-        public static FhirResult SetETagHeader(this FhirResult fhirResult, string eTag)
-        {
-            if (!string.IsNullOrWhiteSpace(eTag))
-            {
-                fhirResult.Headers.Add(HeaderNames.ETag, eTag);
-            }
-
-            return fhirResult;
-        }
-
         public static FhirResult SetLastModifiedHeader(this FhirResult fhirResult)
         {
             var resource = fhirResult.Resource;

diff --git a/src/Microsoft.Health.Fhir.Api/Features/Logging/LogResourceUpsertedEvent.cs b/src/Microsoft.Health.Fhir.Api/Features/Logging/LogResourceUpsertedEvent.cs
diff --git a/src/Microsoft.Health.Fhir.Api/Microsoft.Health.Fhir.Api.csproj b/src/Microsoft.Health.Fhir.Api/Microsoft.Health.Fhir.Api.csproj
@@ -3,16 +3,7 @@
   <PropertyGroup>
     <TargetFramework>netcoreapp2.1</TargetFramework>
     <CodeAnalysisRuleSet>..\..\CustomAnalysisRules.ruleset</CodeAnalysisRuleSet>
-    <TreatWarningsAsErrors>true</TreatWarningsAsErrors>
-    <WarningsAsErrors />
     <DocumentationFile>bin\$(Configuration)\$(TargetFramework)\Microsoft.Health.Fhir.Api.xml</DocumentationFile>
-    <!-- Due to the bug in VS, The DebugType needs to be set to Full for CodeCoverage to work property. Remove after the fix is deployed.-->
-    <DebugType>Full</DebugType>
-    <LangVersion>latest</LangVersion>
-    <HighEntropyVA>true</HighEntropyVA>
-    <PublishRepositoryUrl>true</PublishRepositoryUrl>
-    <EmbedUntrackedSources>true</EmbedUntrackedSources>
-    <AllowedOutputExtensionsInPackageBuildOutputFolder>$(AllowedOutputExtensionsInPackageBuildOutputFolder);.pdb</AllowedOutputExtensionsInPackageBuildOutputFolder>
   </PropertyGroup>
 
   <ItemGroup>

diff --git a/src/Microsoft.Health.Fhir.Api/Modules/MediationModule.cs b/src/Microsoft.Health.Fhir.Api/Modules/MediationModule.cs
@@ -4,11 +4,13 @@
 // -------------------------------------------------------------------------------------------------
 
 using System;
+using System.Linq;
 using EnsureThat;
 using MediatR;
 using MediatR.Pipeline;
 using Microsoft.Extensions.DependencyInjection;
 using Microsoft.Health.Extensions.DependencyInjection;
+using Microsoft.Health.Fhir.Core.Features.Conformance;
 using Microsoft.Health.Fhir.Core.Features.Persistence;
 
 namespace Microsoft.Health.Fhir.Api.Modules
@@ -23,17 +25,29 @@ public void Load(IServiceCollection services)
         {
             EnsureArg.IsNotNull(services, nameof(services));
 
-            var coreAssembly = typeof(IFhirRepository).Assembly;
+            var coreAssembly = typeof(IDataStore).Assembly;
 
             services.AddMediatR(GetType().Assembly, coreAssembly);
             services.AddTransient(typeof(IPipelineBehavior<,>), typeof(RequestPreProcessorBehavior<,>));
             services.AddTransient(typeof(IPipelineBehavior<,>), typeof(RequestPostProcessorBehavior<,>));
 
             Predicate<Type> isPipelineBehavior = y => y.IsGenericType && y.GetGenericTypeDefinition() == typeof(IPipelineBehavior<,>);
 
-            services.TypesInSameAssemblyAs<IFhirRepository>()
+            services.TypesInSameAssemblyAs<IDataStore>()
                 .Transient()
                 .AsImplementedInterfaces(isPipelineBehavior);
+
+            // Allows handlers to provide capabilities
+            var openRequestInterfaces = new Type[]
+            {
+                typeof(IRequestHandler<,>),
+                typeof(INotificationHandler<>),
+            };
+
+            services.TypesInSameAssemblyAs<IDataStore>()
+                .Where(y => y.Type.IsGenericType && openRequestInterfaces.Contains(y.Type.GetGenericTypeDefinition()))
+                .Transient()
+                .AsImplementedInterfaces(x => x == typeof(IProvideCapability));
         }
     }
 }
diff --git a/src/Microsoft.Health.Fhir.Api/Modules/PersistenceModule.cs b/src/Microsoft.Health.Fhir.Api/Modules/PersistenceModule.cs
@@ -21,7 +21,6 @@ public void Load(IServiceCollection services)
         {
             EnsureArg.IsNotNull(services, nameof(services));
 
-            services.AddScoped<IFhirRepository, FhirRepository>();
             services.AddSingleton<IRawResourceFactory, RawResourceFactory>();
             services.AddSingleton<IResourceWrapperFactory, ResourceWrapperFactory>();
             services.AddSingleton<IClaimsIndexer, ClaimsIndexer>();