public GroupMemberExtractorTests()
{
var dataClient = Substitute.For <IFhirDataClient>();
dataClient.SearchAsync(new ResourceIdSearchOptions("Group", _sampleGroupId, null), _noneCancellationToken)
.ReturnsForAnyArgs(x =>
{
var resourceId = ((ResourceIdSearchOptions)x[0]).ResourceId;
var testDataFile = _groupIdToTestDataFile.ContainsKey(resourceId)
? Path.Combine(_testDataFolder, _groupIdToTestDataFile[resourceId])
: TestDataConstants.EmptyBundleFile;
var bundle =
TestDataProvider.GetBundleFromFile(testDataFile);
return(bundle);
});
var fhirServerConfig = new FhirServerConfiguration
{
ServerUrl = "https://example.com",
Authentication = AuthenticationType.None,
};
var fhirServerOption = Options.Create(fhirServerConfig);
_dataSource = new FhirApiDataSource(fhirServerOption);
_referenceParser = new R4ReferenceParser(_dataSource, NullLogger <R4ReferenceParser> .Instance);
_groupMemberExtractor = new GroupMemberExtractor(dataClient, _referenceParser, _nullGroupMemberExtractorLogger);
}
/// <summary>
/// Adds services for enabling a FHIR server.
/// </summary>
/// <param name="services">The services collection.</param>
/// <param name="configurationRoot">An optional configuration root object. This method uses "FhirServer" section.</param>
/// <param name="configureAction">An optional delegate to set <see cref="FhirServerConfiguration"/> properties after values have been loaded from configuration</param>
/// <returns>A <see cref="IFhirServerBuilder"/> object.</returns>
public static IFhirServerBuilder AddFhirServer(
this IServiceCollection services,
IConfiguration configurationRoot = null,
Action <FhirServerConfiguration> configureAction = null)
{
EnsureArg.IsNotNull(services, nameof(services));
services.AddOptions();
services.AddMvc(options =>
{
options.EnableEndpointRouting = false;
options.RespectBrowserAcceptHeader = true;
})
.AddNewtonsoftJson()
.AddRazorRuntimeCompilation();
var fhirServerConfiguration = new FhirServerConfiguration();
configurationRoot?.GetSection(FhirServerConfigurationSectionName).Bind(fhirServerConfiguration);
configureAction?.Invoke(fhirServerConfiguration);
services.AddSingleton(Options.Options.Create(fhirServerConfiguration));
services.AddSingleton(Options.Options.Create(fhirServerConfiguration.Security));
services.AddSingleton(Options.Options.Create(fhirServerConfiguration.Features));
services.AddSingleton(Options.Options.Create(fhirServerConfiguration.CoreFeatures));
services.AddSingleton(Options.Options.Create(fhirServerConfiguration.Cors));
services.AddSingleton(Options.Options.Create(fhirServerConfiguration.Operations));
services.AddSingleton(Options.Options.Create(fhirServerConfiguration.Operations.Export));
services.AddSingleton(Options.Options.Create(fhirServerConfiguration.Operations.Reindex));
services.AddSingleton(Options.Options.Create(fhirServerConfiguration.Operations.ConvertData));
services.AddSingleton(Options.Options.Create(fhirServerConfiguration.Audit));
services.AddSingleton(Options.Options.Create(fhirServerConfiguration.Bundle));
services.AddSingleton(Options.Options.Create(fhirServerConfiguration.Throttling));
services.AddSingleton(Options.Options.Create(fhirServerConfiguration.ArtifactStore));
services.AddTransient <IStartupFilter, FhirServerStartupFilter>();
services.RegisterAssemblyModules(Assembly.GetExecutingAssembly(), fhirServerConfiguration);
services.AddFhirServerBase(fhirServerConfiguration);
services.AddHttpClient(Options.Options.DefaultName)
.AddTransientHttpErrorPolicy(builder =>
builder.OrResult(m => m.StatusCode == HttpStatusCode.TooManyRequests)
.WaitAndRetryAsync(5, retryAttempt => TimeSpan.FromSeconds(Math.Pow(2, retryAttempt))));
var multipleRegisteredServices = services
.GroupBy(x => (x.ServiceType, x.ImplementationType, x.ImplementationInstance, x.ImplementationFactory))
.Where(x => x.Count() > 1)
.ToArray();
if (multipleRegisteredServices.Any())
{
foreach (var service in multipleRegisteredServices)
{
Debug.WriteLine($"** IoC Config Warning: Service implementation '{service.Key.ImplementationType ?? service.Key.ImplementationInstance ?? service.Key.ImplementationFactory}' was registered multiple times.");
}
}
return(new FhirServerBuilder(services));
}
/// <summary>
/// Adds services for enabling a FHIR server.
/// </summary>
/// <param name="services">The services collection.</param>
/// <param name="configurationRoot">An optional configuration root object. This method uses "FhirServer" section.</param>
/// <param name="configureAction">An optional delegate to set <see cref="FhirServerConfiguration"/> properties after values have been loaded from configuration</param>
/// <returns>A <see cref="IFhirServerBuilder"/> object.</returns>
public static IFhirServerBuilder AddFhirServer(
this IServiceCollection services,
IConfiguration configurationRoot = null,
Action <FhirServerConfiguration> configureAction = null)
{
EnsureArg.IsNotNull(services, nameof(services));
services.AddOptions();
services.AddMvc(options =>
{
options.RespectBrowserAcceptHeader = true;
});
var fhirServerConfiguration = new FhirServerConfiguration();
configurationRoot?.GetSection(FhirServerConfigurationSectionName).Bind(fhirServerConfiguration);
configureAction?.Invoke(fhirServerConfiguration);
services.AddSingleton(Options.Options.Create(fhirServerConfiguration));
services.AddSingleton(Options.Options.Create(fhirServerConfiguration.Security));
services.AddSingleton(Options.Options.Create(fhirServerConfiguration.Conformance));
services.AddSingleton(Options.Options.Create(fhirServerConfiguration.Features));
services.AddSingleton(Options.Options.Create(fhirServerConfiguration.Cors));
services.AddTransient <IStartupFilter, FhirServerStartupFilter>();
services.RegisterAssemblyModules(Assembly.GetExecutingAssembly(), fhirServerConfiguration);
services.AddHttpClient();
return(new FhirServerBuilder(services));
}
public void GivenEmptyServerUrl_WhenInitialize_ArgumentExceptionShouldBeThrown()
{
// ServerUrl is string.empty
var fhirServerConfig = new FhirServerConfiguration();
Assert.Throws <ArgumentException>(() => new FhirApiDataSource(Options.Create(fhirServerConfig)));
fhirServerConfig.ServerUrl = "";
Assert.Throws <ArgumentException>(() => new FhirApiDataSource(Options.Create(fhirServerConfig)));
}
private ITypedElement GetTestElement(string fileName)
{
var fhirConfiguration = new FhirServerConfiguration()
{
Version = FhirVersion.R4,
};
var fhirParser = new FhirSerializer(Options.Create(fhirConfiguration));
return(fhirParser.DeserializeToElement(File.ReadAllText(fileName)));
}
public void GivenServerUrl_WhenInitialize_ServerUrlShouldBeEndsWithSlash(string serverUrl, string expectedServerUrl)
{
var fhirServerConfig = new FhirServerConfiguration
{
ServerUrl = serverUrl,
};
var dataSource = new FhirApiDataSource(Options.Create(fhirServerConfig));
Assert.Equal(expectedServerUrl, dataSource.FhirServerUrl);
}
/// <summary>
/// Adds services for enabling a FHIR server.
/// </summary>
/// <param name="services">The services collection.</param>
/// <param name="configurationRoot">An optional configuration root object. This method uses "FhirServer" section.</param>
/// <param name="configureAction">An optional delegate to set <see cref="FhirServerConfiguration"/> properties after values have been loaded from configuration</param>
/// <returns>A <see cref="IFhirServerBuilder"/> object.</returns>
public static IFhirServerBuilder AddFhirServer(
this IServiceCollection services,
IConfiguration configurationRoot = null,
Action <FhirServerConfiguration> configureAction = null)
{
EnsureArg.IsNotNull(services, nameof(services));
services.AddOptions();
services.AddMvc(options =>
{
options.EnableEndpointRouting = false;
options.RespectBrowserAcceptHeader = true;
})
.AddNewtonsoftJson()
.AddRazorRuntimeCompilation();
var fhirServerConfiguration = new FhirServerConfiguration();
configurationRoot?.GetSection(FhirServerConfigurationSectionName).Bind(fhirServerConfiguration);
configureAction?.Invoke(fhirServerConfiguration);
services.AddSingleton(Options.Options.Create(fhirServerConfiguration));
services.AddSingleton(Options.Options.Create(fhirServerConfiguration.Security));
services.AddSingleton(Options.Options.Create(fhirServerConfiguration.Features));
services.AddSingleton(Options.Options.Create(fhirServerConfiguration.CoreFeatures));
services.AddSingleton(Options.Options.Create(fhirServerConfiguration.Cors));
services.AddSingleton(Options.Options.Create(fhirServerConfiguration.Operations));
services.AddSingleton(Options.Options.Create(fhirServerConfiguration.Operations.Export));
services.AddSingleton(Options.Options.Create(fhirServerConfiguration.Audit));
services.AddSingleton(Options.Options.Create(fhirServerConfiguration.Bundle));
services.AddTransient <IStartupFilter, FhirServerStartupFilter>();
services.RegisterAssemblyModules(Assembly.GetExecutingAssembly(), fhirServerConfiguration);
services.AddFhirServerBase(fhirServerConfiguration);
services.AddHttpClient();
var multipleRegisteredServices = services
.GroupBy(x => (x.ServiceType, x.ImplementationType, x.ImplementationInstance, x.ImplementationFactory))
.Where(x => x.Count() > 1)
.ToArray();
if (multipleRegisteredServices.Any())
{
foreach (var service in multipleRegisteredServices)
{
Debug.WriteLine($"** IoC Config Warning: Service implementation '{service.Key.ImplementationType ?? service.Key.ImplementationInstance ?? service.Key.ImplementationFactory}' was registered multiple times.");
}
}
return(new FhirServerBuilder(services));
}
public R4ReferenceParserTests()
{
var fhirServerConfig = new FhirServerConfiguration
{
ServerUrl = _serverUrl,
Authentication = AuthenticationType.None,
};
var fhirServerOption = Options.Create(fhirServerConfig);
_dataSource = new FhirApiDataSource(fhirServerOption);
_referenceParser = new R4ReferenceParser(_dataSource, _nullR4ReferenceParserLogger);
}
public static ITypedElement GetBundleElementFromFile(string filePath)
{
var bundleContent = GetBundleFromFile(filePath);
var fhirConfiguration = new FhirServerConfiguration()
{
Version = FhirVersion.R4,
};
var fhirSerializer = new FhirSerializer(Options.Create(fhirConfiguration));
return(fhirSerializer.DeserializeToElement(bundleContent));
}
public void GivenDataSourceServerUrlEndsWithSlash_WhenParseReference_ParsedReferenceShouldBeReturned()
{
var fhirServerConfig = new FhirServerConfiguration
{
ServerUrl = "https://example.com/",
Authentication = AuthenticationType.None,
};
var fhirServerOption = Options.Create(fhirServerConfig);
var dataSource = new FhirApiDataSource(fhirServerOption);
var referenceParser = new R4ReferenceParser(dataSource, _nullR4ReferenceParserLogger);
var fhirReference = referenceParser.Parse("https://example.com/Patient/123/_history/2");
Assert.NotNull(fhirReference);
Assert.Equal("Patient", fhirReference.ResourceType);
Assert.Equal("123", fhirReference.ResourceId);
}
/// <summary>
/// Adds services for enabling a FHIR server.
/// </summary>
/// <param name="services">The services collection.</param>
/// <param name="configurationRoot">An optional configuration root object. This method uses "FhirServer" section.</param>
/// <param name="configureAction">An optional delegate to set <see cref="FhirServerConfiguration"/> properties after values have been loaded from configuration</param>
/// <returns>A <see cref="IFhirServerBuilder"/> object.</returns>
public static IFhirServerBuilder AddFhirServer(
this IServiceCollection services,
IConfiguration configurationRoot = null,
Action <FhirServerConfiguration> configureAction = null)
{
EnsureArg.IsNotNull(services, nameof(services));
services.AddOptions();
services.AddMvc(options =>
{
options.EnableEndpointRouting = false;
options.RespectBrowserAcceptHeader = true;
})
.AddNewtonsoftJson()
.AddRazorRuntimeCompilation();
var fhirServerConfiguration = new FhirServerConfiguration();
configurationRoot?.GetSection(FhirServerConfigurationSectionName).Bind(fhirServerConfiguration);
configureAction?.Invoke(fhirServerConfiguration);
services.AddSingleton(Options.Options.Create(fhirServerConfiguration));
services.AddSingleton(Options.Options.Create(fhirServerConfiguration.Security));
services.AddSingleton(Options.Options.Create(fhirServerConfiguration.Features));
services.AddSingleton(Options.Options.Create(fhirServerConfiguration.CoreFeatures));
services.AddSingleton(Options.Options.Create(fhirServerConfiguration.Cors));
services.AddSingleton(Options.Options.Create(fhirServerConfiguration.Operations));
services.AddSingleton(Options.Options.Create(fhirServerConfiguration.Operations.Export));
services.AddSingleton(Options.Options.Create(fhirServerConfiguration.Audit));
services.AddSingleton(Options.Options.Create(fhirServerConfiguration.Bundle));
services.AddTransient <IStartupFilter, FhirServerStartupFilter>();
services.RegisterAssemblyModules(Assembly.GetExecutingAssembly(), fhirServerConfiguration);
services.AddFhirServerBase(fhirServerConfiguration);
services.AddHttpClient();
return(new FhirServerBuilder(services));
}
public CorsModule(FhirServerConfiguration fhirServerConfiguration)
{
EnsureArg.IsNotNull(fhirServerConfiguration, nameof(fhirServerConfiguration));
_corsConfiguration = fhirServerConfiguration.Cors;
}
public FhirModule(FhirServerConfiguration fhirServerConfiguration)
{
EnsureArg.IsNotNull(fhirServerConfiguration, nameof(fhirServerConfiguration));
_featureConfiguration = fhirServerConfiguration.Features;
}
public override void Configure(IFunctionsHostBuilder builder)
{
var services = builder.Services;
/* Hack to get IConfiguration */
var serviceProvider = builder.Services.BuildServiceProvider();
var configurationRoot = serviceProvider.GetService <IConfiguration>();
var env = serviceProvider.GetRequiredService <IHostEnvironment>();
var appDirectory = serviceProvider.GetRequiredService <IOptions <ExecutionContextOptions> >().Value.AppDirectory;
var configBuilder = new ConfigurationBuilder()
.SetBasePath(appDirectory)
.AddJsonFile("appsettings.json");
var customConfig = configBuilder.AddConfiguration(configurationRoot).Build();
services.AddOptions();
services.Add <IConfiguration>(x => customConfig).Singleton().ReplaceService <IConfiguration>();
var fhirServerConfiguration = new FhirServerConfiguration();
customConfig?.GetSection(FhirServerConfigurationSectionName).Bind(fhirServerConfiguration);
services.AddSingleton(Options.Create(fhirServerConfiguration));
services.AddSingleton(Options.Create(fhirServerConfiguration.Security));
services.AddSingleton(Options.Create(fhirServerConfiguration.Features));
services.AddSingleton(Options.Create(fhirServerConfiguration.CoreFeatures));
services.AddSingleton(Options.Create(fhirServerConfiguration.Cors));
services.AddSingleton(Options.Create(fhirServerConfiguration.Operations));
services.AddSingleton(Options.Create(fhirServerConfiguration.Operations.Export));
services.AddSingleton(Options.Create(fhirServerConfiguration.Operations.Reindex));
services.AddSingleton(Options.Create(fhirServerConfiguration.Audit));
services.AddSingleton(Options.Create(fhirServerConfiguration.Bundle));
services.AddSingleton(Options.Create(fhirServerConfiguration.Throttling));
new FhirModule(fhirServerConfiguration).Load(services);
services.RemoveAll(typeof(IScoped <>));
services.AddTransient(typeof(IScoped <>), typeof(FunctionsScoped <>));
new MediationModule().Load(services);
new PersistenceModule().Load(services);
new SearchModule(fhirServerConfiguration).Load(services);
new ValidationModule().Load(services);
services.TryAddSingleton <IHttpContextAccessor, HttpContextAccessor>();
services.Add <QueryStringParser>().Singleton().AsService <IQueryStringParser>();
services.Add <FunctionsUrlResolver>().Singleton().ReplaceService <IUrlResolver>();
services.AddHttpClient();
services.Add <StartupExtension>().Transient().AsImplementedInterfaces();
string dataStore = customConfig["DataStore"];
if (dataStore.Equals("CosmosDb", StringComparison.InvariantCultureIgnoreCase))
{
var fhirBuilder = new FunctionsFhirServerBuilder(services);
fhirBuilder.AddCosmosDbCore();
}
}
public static IServiceCollection AddFhirServerBase(this IServiceCollection services, FhirServerConfiguration fhirServerConfiguration)
{
EnsureArg.IsNotNull(services, nameof(services));
EnsureArg.IsNotNull(fhirServerConfiguration, nameof(fhirServerConfiguration));
services.RegisterAssemblyModules(Assembly.GetExecutingAssembly(), fhirServerConfiguration);
services.RegisterAssemblyModules(typeof(InitializationModule).Assembly, fhirServerConfiguration);
return(services);
}
public SearchModule(FhirServerConfiguration configuration)
{
EnsureArg.IsNotNull(configuration, nameof(configuration));
_configuration = configuration;
}
public SecurityModule(FhirServerConfiguration fhirServerConfiguration)
{
EnsureArg.IsNotNull(fhirServerConfiguration, nameof(fhirServerConfiguration));
_securityConfiguration = fhirServerConfiguration.Security;
}
public ControlPlaneModule(FhirServerConfiguration fhirServerConfiguration)
{
EnsureArg.IsNotNull(fhirServerConfiguration, nameof(fhirServerConfiguration));
}
