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Adds a local copy of the npm packages for the validator #3241

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Adds a local copy of the npm packages for the validator #3241

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066058b
Uses fhir npm packages for validation
brendankowitz Feb 9, 2023
9f720a7
Add local npm packages for validation
feordin Apr 19, 2023
67b5f92
Fix bug identifying correct npm package files.
feordin Apr 20, 2023
255276b
Skip tests for R5 as they are not fully functioning
feordin Apr 20, 2023
9126fdc
Add R5 check, and firely SDK version check
feordin Apr 21, 2023
ec52987
fix accidental change to appsettings.json
feordin Apr 24, 2023
8ae853c
Read packages from local npm feed
feordin May 9, 2023
de641e4
Update Skip check
feordin May 9, 2023
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5 changes: 1 addition & 4 deletions src/Microsoft.Health.Fhir.R4.Api/Microsoft.Health.Fhir.R4.Api.csproj
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Original file line number Diff line number Diff line change
@@ -1,13 +1,10 @@
<Project Sdk="Microsoft.NET.Sdk">
<Project Sdk="Microsoft.NET.Sdk">
<PropertyGroup>
<RootNamespace>Microsoft.Health.Fhir.Api</RootNamespace>
</PropertyGroup>
<PropertyGroup>
<DefineConstants>R4</DefineConstants>
</PropertyGroup>
<ItemGroup>
<Content Remove="C:\Users\jaerwin\.nuget\packages\hl7.fhir.specification.r4\4.3.0\contentFiles\any\any\specification.zip" />
</ItemGroup>
<ItemGroup>
<Compile Include="..\Microsoft.Health.Fhir.Shared.Api\Modules\AnonymizationModule.cs" Link="Modules\AnonymizationModule.cs" />
</ItemGroup>
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3 changes: 0 additions & 3 deletions src/Microsoft.Health.Fhir.R4B.Api/Microsoft.Health.Fhir.R4B.Api.csproj
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Expand Up @@ -5,9 +5,6 @@
<PropertyGroup>
<DefineConstants>R4;R4B</DefineConstants>
</PropertyGroup>
<ItemGroup>
<Content Remove="C:\Users\jaerwin\.nuget\packages\hl7.fhir.specification.r4b\4.3.0\contentFiles\any\any\specification.zip" />
</ItemGroup>

<ItemGroup>
<PackageReference Include="Ensure.That" />
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3 changes: 0 additions & 3 deletions src/Microsoft.Health.Fhir.R5.Api/Microsoft.Health.Fhir.R5.Api.csproj
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Expand Up @@ -5,9 +5,6 @@
<PropertyGroup>
<DefineConstants>R5</DefineConstants>
</PropertyGroup>
<ItemGroup>
<Content Remove="C:\Users\jaerwin\.nuget\packages\hl7.fhir.specification.r5\4.3.0\contentFiles\any\any\specification.zip" />
</ItemGroup>

<ItemGroup>
<PackageReference Include="Ensure.That" />
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17 changes: 15 additions & 2 deletions src/Microsoft.Health.Fhir.Shared.Core/Features/Validation/ProfileValidator.cs
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Expand Up @@ -63,9 +63,11 @@ private IResourceResolver Initialize()
packagesToInclude.Add(packageVariables.CorePackageName);
packagesToInclude.Add(packageVariables.ExpansionsPackageName);

#if !R5
// elements package name is not included in the reflection metadata, but we should try and include it
var extensionsPackageName = packageVariables.ExpansionsPackageName.Replace("expansions", "elements", StringComparison.OrdinalIgnoreCase);
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packagesToInclude.Add(extensionsPackageName);
#endif
}

foreach (var package in _coreConfig.PackageConfiguration.PackageNames)
Expand All @@ -80,9 +82,20 @@ private IResourceResolver Initialize()
{
// Allow local packages
var resolvedPath = Path.GetFullPath(_coreConfig.PackageConfiguration.PackageSource, Environment.CurrentDirectory);
validationSource = new FhirPackageSource(Directory.GetFiles(resolvedPath)

var packageFileList = Directory.GetFiles(resolvedPath)
.Where(f => packagesToInclude.Any(p => f.Contains(p, StringComparison.OrdinalIgnoreCase)
&& f.EndsWith("tgz", StringComparison.OrdinalIgnoreCase))).ToArray());
&& f.EndsWith("tgz", StringComparison.OrdinalIgnoreCase))).ToArray();

if (packageFileList.Length != packagesToInclude.Count)
{
_logger.LogWarning(
"Attempted to load {DesiredPackageList} packages, but found {ActualPackageList} in file system.",
string.Join(',', packagesToInclude),
string.Join(',', packageFileList));
}

validationSource = new FhirPackageSource(packageFileList);
}
else
{
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2 changes: 1 addition & 1 deletion src/Microsoft.Health.Fhir.Shared.Web/appsettings.json
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@@ -1,7 +1,7 @@
{
"FhirServer": {
"Security": {
"Enabled": true,
"Enabled": false,
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"EnableAadSmartOnFhirProxy": true,
"Authentication": {
"Audience": null,
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4 changes: 0 additions & 4 deletions src/Microsoft.Health.Fhir.Stu3.Api/Microsoft.Health.Fhir.Stu3.Api.csproj
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Expand Up @@ -8,10 +8,6 @@
<DefineConstants>STU3</DefineConstants>
</PropertyGroup>

<ItemGroup>
<Content Remove="C:\Users\jaerwin\.nuget\packages\hl7.fhir.specification.stu3\4.3.0\contentFiles\any\any\specification.zip" />
</ItemGroup>

<ItemGroup>
<Compile Include="..\Microsoft.Health.Fhir.Shared.Api\Modules\AnonymizationModule.cs" Link="Modules\AnonymizationModule.cs" />
</ItemGroup>
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6 changes: 4 additions & 2 deletions test/Microsoft.Health.Fhir.Shared.Tests.E2E/Rest/BatchTests.cs
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Expand Up @@ -6,10 +6,10 @@
using System.Collections.Generic;
using System.Linq;
using System.Net;
using System.Reflection;
using Hl7.Fhir.Model;
using Microsoft.Health.Fhir.Client;
using Microsoft.Health.Fhir.Core.Extensions;
using Microsoft.Health.Fhir.Core.Models;
using Microsoft.Health.Fhir.Tests.Common;
using Microsoft.Health.Fhir.Tests.Common.FixtureParameters;
using Microsoft.Health.Fhir.Tests.E2E.Common;
Expand All @@ -27,6 +27,7 @@ namespace Microsoft.Health.Fhir.Tests.E2E.Rest
public class BatchTests : IClassFixture<HttpIntegrationTestFixture>
{
private readonly TestFhirClient _client;
private readonly int _firelySdkVersion;
private readonly Dictionary<HttpStatusCode, string> _statusCodeMap = new Dictionary<HttpStatusCode, string>()
{
{ HttpStatusCode.NoContent, "204" },
Expand All @@ -40,6 +41,7 @@ public class BatchTests : IClassFixture<HttpIntegrationTestFixture>
public BatchTests(HttpIntegrationTestFixture fixture)
{
_client = fixture.TestFhirClient;
_firelySdkVersion = Assembly.GetAssembly(typeof(Hl7.Fhir.Model.Resource)).GetName().Version.Major;
}

[Fact]
Expand Down Expand Up @@ -178,7 +180,7 @@ private void ValidateOperationOutcome(string actualStatusCode, OperationOutcome
[InlineData(false)]
public async Task GivenABatchBundle_WithProfileValidationFlag_ReturnsABundleResponse(bool profileValidation)
{
Skip.If(ModelInfoProvider.Instance.Version == FhirSpecification.R5, "Validation not currently working correctly for R5");
Skip.If(_firelySdkVersion < 5, "Validation not currently working correctly for R5 previous to firely version 5");

var bundle = new Hl7.Fhir.Model.Bundle
{
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10 changes: 6 additions & 4 deletions test/Microsoft.Health.Fhir.Shared.Tests.E2E/Rest/ValidateTests.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -6,12 +6,12 @@
using System;
using System.Linq;
using System.Net;
using System.Reflection;
using Hl7.Fhir.ElementModel;
using Hl7.Fhir.Model;
using Hl7.Fhir.Serialization;
using Microsoft.Health.Fhir.Client;
using Microsoft.Health.Fhir.Core.Extensions;
using Microsoft.Health.Fhir.Core.Models;
using Microsoft.Health.Fhir.Tests.Common;
using Microsoft.Health.Fhir.Tests.Common.FixtureParameters;
using Microsoft.Health.Fhir.Tests.E2E.Common;
Expand All @@ -27,10 +27,12 @@ public class ValidateTests : IClassFixture<ValidateTestFixture>
{
private const string Success = "All OK";
private readonly TestFhirClient _client;
private readonly int _firelySdkVersion;

public ValidateTests(ValidateTestFixture fixture)
{
_client = fixture.TestFhirClient;
_firelySdkVersion = Assembly.GetAssembly(typeof(Hl7.Fhir.Model.Resource)).GetName().Version.Major;
}

[SkippableTheory]
Expand All @@ -44,7 +46,7 @@ public ValidateTests(ValidateTestFixture fixture)
[InlineData("CarePlan/$validate", "Profile-CarePlan-uscore", null)]
public async void GivenAValidateRequest_WhenTheResourceIsValid_ThenAnOkMessageIsReturned(string path, string filename, string profile)
{
Skip.If(ModelInfoProvider.Instance.Version == FhirSpecification.R5, "Validation not currently working correctly for R5");
Skip.If(_firelySdkVersion < 5, "Validation not currently working correctly for R5 previous to firely version 5");

OperationOutcome outcome = await _client.ValidateAsync(path, Samples.GetJson(filename), profile);

Expand Down Expand Up @@ -140,7 +142,7 @@ public async void GivenAValidateRequest_WhenTheResourceIsInvalid_ThenADetailedEr
[SkippableFact]
public async void GivenAValidateByIdRequest_WhenTheResourceIsValid_ThenAnOkMessageIsReturned()
{
Skip.If(ModelInfoProvider.Instance.Version == FhirSpecification.R5, "Validation not currently working correctly for R5");
Skip.If(_firelySdkVersion < 5, "Validation not currently working correctly for R5 previous to firely version 5");

var fhirSource = Samples.GetJson("Profile-Patient-uscore");
var parser = new FhirJsonParser();
Expand Down Expand Up @@ -172,7 +174,7 @@ public async void GivenAValidateByIdRequestWithStricterProfile_WhenRunningValida
[SkippableFact]
public async void GivenAValidateRequest_WhenAValidResourceIsPassedByParameter_ThenAnOkMessageIsReturned()
{
Skip.If(ModelInfoProvider.Instance.Version == FhirSpecification.R5, "Validation not currently working correctly for R5");
Skip.If(_firelySdkVersion < 5, "Validation not currently working correctly for R5 previous to firely version 5");

var payload = "{\"resourceType\": \"Parameters\", \"parameter\": [{\"name\": \"resource\", \"resource\": {\"resourceType\": \"Patient\", \"id\": \"123\"}}]}";

Expand Down