HL7v2 MLLP Listener (#103)

* gh-8 initial implementation of HL7 MLLP Frame listener
* gh-8 Update integration test

Signed-off-by: Victor Chang <[email protected]>

Author: mocsharp

.github/containerscan/allowedlist.yaml

@@ -14,4 +14,4 @@
 
 general:
   vulnerabilities:
-    - CVE-2018-8292
+    - CVE-2018-8292

.gitignore

@@ -20,7 +20,7 @@
 *.db
 *.db-*
 src/InformaticsGateway/payloads
-
+.run/
 # docfx temp files
 _site/
 
@@ -559,4 +559,4 @@ FodyWeavers.xsd
 ### VisualStudio Patch ###
 # Additional files built by Visual Studio
 
-# End of https://www.toptal.com/developers/gitignore/api/aspnetcore,dotnetcore,visualstudio,visualstudiocode
+# End of https://www.toptal.com/developers/gitignore/api/aspnetcore,dotnetcore,visualstudio,visualstudiocode

docker-compose/docker-compose.dev.yml

@@ -0,0 +1,71 @@
+# Copyright 2022 MONAI Consortium
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+version: "3.7"
+services:
+  rabbitmq:
+    image: rabbitmq:3-management
+    hostname: rabbitmq
+    ports:
+        - 5672:5672
+        - 15672:15672
+    environment:
+        RABBITMQ_DEFAULT_USER: "rabbitmq"
+        RABBITMQ_DEFAULT_PASS: "rabbitmq"
+        RABBITMQ_DEFAULT_VHOST: "monaideploy"
+        RABBITMQ_ERLANG_COOKIE: "SWQOKODSQALRPCLNMEQG"
+
+    healthcheck:
+      test: rabbitmq-diagnostics -q ping
+      interval: 15s
+      timeout: 30s
+      retries: 3
+
+  minio:
+    image: "minio/minio:latest"
+    command: server --console-address ":9001" /data
+    hostname: minio
+    volumes:
+      - ./.run/minio/data:/data
+      - ./.run/minio/config:/root/.minio
+    ports:
+      - "9000:9000"
+    environment:
+      MINIO_ROOT_USER: minioadmin
+      MINIO_ROOT_PASSWORD: minioadmin
+    healthcheck:
+      test: ["CMD", "curl", "-f", "http://localhost:9000/minio/health/live"]
+      interval: 15s
+      timeout: 30s
+      retries: 3
+
+  createbuckets:
+    image: minio/mc
+    environment:
+      MINIO_ROOT_USER: minioadmin
+      MINIO_ROOT_PASSWORD: minioadmin
+      BUCKET_NAME: monaideploy
+      ENDPOINT: http://minio:9000
+    depends_on:
+      minio:
+        condition: service_healthy
+    entrypoint: >
+      /bin/sh -c "
+      until (/usr/bin/mc config host add myminio $$ENDPOINT $$MINIO_ROOT_USER $$MINIO_ROOT_PASSWORD) do echo '...waiting...' && sleep 1; done;
+      /usr/bin/mc mb myminio/$$BUCKET_NAME;
+      /usr/bin/mc policy set public myminio/$$BUCKET_NAME;
+      /usr/bin/mc ls myminio;
+      # exit 0
+      "
+

src/Api/Monai.Deploy.InformaticsGateway.Api.csproj

@@ -31,7 +31,7 @@
     <PackageReference Include="Macross.Json.Extensions" Version="3.0.0" />
     <PackageReference Include="Microsoft.EntityFrameworkCore.Abstractions" Version="6.0.7" />
     <PackageReference Include="Monai.Deploy.Messaging" Version="0.1.3-rc0010" />
-    <PackageReference Include="Monai.Deploy.Storage" Version="0.2.0-rc0012" />
+    <PackageReference Include="Monai.Deploy.Storage" Version="0.2.0-rc0014" />
     <PackageReference Include="System.ComponentModel.Annotations" Version="5.0.0" />
   </ItemGroup>
 

src/Configuration/ConfigurationValidator.cs

@@ -54,6 +54,7 @@ public ValidateOptionsResult Validate(string name, InformaticsGatewayConfigurati
             valid &= IsDicomWebValid(options.DicomWeb);
             valid &= IsFhirValid(options.Fhir);
             valid &= IsStorageValid(options.Storage);
+            valid &= IsHl7Valid(options.Hl7);
 
 #pragma warning disable CA2254 // Template should be a static expression
             _validationErrors.ForEach(p => _logger.Log(LogLevel.Error, p));
@@ -62,6 +63,14 @@ public ValidateOptionsResult Validate(string name, InformaticsGatewayConfigurati
             return valid ? ValidateOptionsResult.Success : ValidateOptionsResult.Fail(string.Join(Environment.NewLine, _validationErrors));
         }
 
+        private bool IsHl7Valid(Hl7Configuration hl7)
+        {
+            var valid = true;
+
+            valid &= ValidationExtensions.IsPortValid("InformaticsGateway>hl7>port", hl7.Port, _validationErrors);
+            return valid;
+        }
+
         private bool IsStorageValid(StorageConfiguration storage)
         {
             var valid = true;

src/Configuration/Hl7Configuration.cs

@@ -0,0 +1,46 @@
+// SPDX-FileCopyrightText: © 2022 MONAI Consortium
+// SPDX-License-Identifier: Apache License 2.0
+
+using Microsoft.Extensions.Configuration;
+
+namespace Monai.Deploy.InformaticsGateway.Configuration
+{
+    public class Hl7Configuration
+    {
+        public static readonly int DefaultClientTimeout = 300000;
+        public const int DefaultMaximumNumberOfConnections = 10;
+
+        /// <summary>
+        /// Gets or sets the client connection timeout in milliseconds.
+        /// </summary>
+        [ConfigurationKeyName("clientTimeout")]
+        public int ClientTimeoutMilliseconds { get; set; } = DefaultClientTimeout;
+
+        /// <summary>
+        /// Gets or sets maximum number of concurrent connections for the HL7 service.
+        /// Defaults to 10.
+        /// </summary>
+        [ConfigurationKeyName("maximumNumberOfConnections")]
+        public int MaximumNumberOfConnections { get; set; } = DefaultMaximumNumberOfConnections;
+
+        /// <summary>
+        /// Gets or sets the MLLP listening port.
+        /// Defaults to 2575.
+        /// </summary>
+        [ConfigurationKeyName("clientTimeout")]
+        public int Port { get; set; } = 2575;
+
+        /// <summary>
+        /// Gets or sets wether to respond with an ack/nack message.
+        /// Defaults to true.
+        /// </summary>
+        [ConfigurationKeyName("sendAck")]
+        public bool SendAcknowledgment { get; set; } = true;
+
+        public uint BufferSize { get; set; } = 10240;
+
+        public Hl7Configuration()
+        {
+        }
+    }
+}

src/Configuration/InformaticsGatewayConfiguration.cs

@@ -56,6 +56,13 @@ public class InformaticsGatewayConfiguration
         [ConfigurationKeyName("fhir")]
         public FhirConfiguration Fhir { get; set; }
 
+        /// <summary>
+        /// Represents the <c>hl7</c> section of the configuration file.
+        /// </summary>
+        /// <value></value>
+        [ConfigurationKeyName("hl7")]
+        public Hl7Configuration Hl7 { get; set; }
+
         /// <summary>
         /// Represents the <c>export</c> section of the configuration file.
         /// </summary>
@@ -83,6 +90,7 @@ public InformaticsGatewayConfiguration()
             Export = new DataExportConfiguration();
             Messaging = new MessageBrokerConfiguration();
             Database = new DatabaseConfiguration();
+            Hl7 = new Hl7Configuration();
         }
     }
 }

src/Configuration/Monai.Deploy.InformaticsGateway.Configuration.csproj

@@ -31,7 +31,7 @@
     <PackageReference Include="Microsoft.Extensions.Logging.Abstractions" Version="6.0.1" />
     <PackageReference Include="Microsoft.Extensions.Options" Version="6.0.0" />
     <PackageReference Include="Monai.Deploy.Messaging" Version="0.1.3-rc0010" />
-    <PackageReference Include="Monai.Deploy.Storage" Version="0.2.0-rc0012" />
+    <PackageReference Include="Monai.Deploy.Storage" Version="0.2.0-rc0014" />
     <PackageReference Include="System.IO.Abstractions" Version="17.0.24" />
   </ItemGroup>
 

src/InformaticsGateway/Logging/Log.800.Hl7Service.cs

@@ -0,0 +1,35 @@
+// SPDX-FileCopyrightText: © 2022 MONAI Consortium
+// SPDX-License-Identifier: Apache License 2.0
+
+using System;
+using Microsoft.Extensions.Logging;
+
+namespace Monai.Deploy.InformaticsGateway.Logging
+{
+    public static partial class Log
+    {
+        [LoggerMessage(EventId = 800, Level = LogLevel.Information, Message = "New HL7 client connected.")]
+        public static partial void ClientConnected(this ILogger logger);
+
+        [LoggerMessage(EventId = 801, Level = LogLevel.Error, Message = "Error reading data, connection may be dropped.")]
+        public static partial void ExceptionReadingClientStream(this ILogger logger, Exception ex);
+
+        [LoggerMessage(EventId = 802, Level = LogLevel.Error, Message = "Error parsing HL7 message.")]
+        public static partial void ErrorParsingHl7Message(this ILogger logger, Exception ex);
+
+        [LoggerMessage(EventId = 803, Level = LogLevel.Warning, Message = "Unable to locate {segment} field {field} in the HL7 message.")]
+        public static partial void MissingFieldInHL7Message(this ILogger logger, string segment, int field, Exception ex);
+
+        [LoggerMessage(EventId = 804, Level = LogLevel.Error, Message = "Error sending HL7 acknowledgment.")]
+        public static partial void ErrorSendingHl7Acknowledgment(this ILogger logger, Exception ex);
+
+        [LoggerMessage(EventId = 805, Level = LogLevel.Information, Message = "Maximum number {maximumAllowedConcurrentConnections} of clients reached.")]
+        public static partial void MaxedOutHl7Connections(this ILogger logger, int maximumAllowedConcurrentConnections);
+
+        [LoggerMessage(EventId = 806, Level = LogLevel.Information, Message = "HL7 listening on port: {port}.")]
+        public static partial void Hl7ListeningOnPort(this ILogger logger, int port);
+
+        [LoggerMessage(EventId = 807, Level = LogLevel.Critical, Message = "Socket error: {error}")]
+        public static partial void Hl7SocketException(this ILogger logger, string error);
+    }
+}

src/InformaticsGateway/Monai.Deploy.InformaticsGateway.csproj

@@ -1,4 +1,4 @@
-<!--
+<!--
   ~ Copyright 2022 MONAI Consortium
   ~
   ~ Licensed under the Apache License, Version 2.0 (the "License");
@@ -36,6 +36,7 @@
         <PackageReference Include="DotNext.Threading" Version="4.6.1" />
         <PackageReference Include="fo-dicom" Version="5.0.2" />
         <PackageReference Include="Karambolo.Extensions.Logging.File" Version="3.3.1" />
+        <PackageReference Include="HL7-dotnetcore" Version="2.29.0" />
         <PackageReference Include="GitVersion.MsBuild" Version="5.10.3">
             <PrivateAssets>All</PrivateAssets>
           </PackageReference>
@@ -45,7 +46,9 @@
         <PackageReference Include="Microsoft.Extensions.Logging" Version="6.0.0" />
         <PackageReference Include="Microsoft.Extensions.Logging.Console" Version="6.0.0" />
         <PackageReference Include="Microsoft.Extensions.Options" Version="6.0.0" />
-        <PackageReference Include="Monai.Deploy.Storage" Version="0.2.0-rc0012" />
+        <PackageReference Include="Monai.Deploy.Messaging.RabbitMQ" Version="0.1.3-rc0010" />
+        <PackageReference Include="Monai.Deploy.Storage" Version="0.2.0-rc0014" />
+        <PackageReference Include="Monai.Deploy.Storage.MinIO" Version="0.2.0-rc0014" />
         <PackageReference Include="Polly" Version="7.2.3" />
         <PackageReference Include="Swashbuckle.AspNetCore" Version="6.4.0" />
     </ItemGroup>
@@ -78,4 +81,20 @@
     <None Include="./appsettings.json" CopyToOutputDirectory="Always" />
     <None Include="./appsettings.Development.json" CopyToOutputDirectory="Always" />
   </ItemGroup>
+
+  <Target Name="CopyPlugins" AfterTargets="AfterPublish">
+    <ItemGroup>
+      <PluginDlls Include="$(PublishDir)Monai.Deploy.Messaging.RabbitMQ.dll;$(PublishDir)Monai.Deploy.Storage.MinIO.dll;$(PublishDir)Minio.dll" />
+    </ItemGroup>
+    <Copy SourceFiles="@(PluginDlls)" DestinationFolder="$(PublishDir)\plug-ins\" SkipUnchangedFiles="true" />
+    <Message Text="Files copied successfully to $(PublishDir)\plug-ins\." Importance="high" />
+  </Target>
+
+  <Target Name="CopyPluginsBuild" AfterTargets="Build">
+    <ItemGroup>
+      <PluginDlls Include="$(OutDir)Monai.Deploy.Messaging.RabbitMQ.dll;$(OutDir)Monai.Deploy.Storage.MinIO.dll;$(OutDir)Minio.dll" />
+    </ItemGroup>
+    <Copy SourceFiles="@(PluginDlls)" DestinationFolder="$(OutDir)\plug-ins\" SkipUnchangedFiles="true" />
+    <Message Text="Files copied successfully to $(OutDir)\plug-ins\." Importance="high" />
+  </Target>
 </Project>

src/InformaticsGateway/Program.cs

@@ -30,9 +30,11 @@
 using Monai.Deploy.InformaticsGateway.Configuration;
 using Monai.Deploy.InformaticsGateway.Database;
 using Monai.Deploy.InformaticsGateway.Repositories;
+using Monai.Deploy.InformaticsGateway.Services.Common;
 using Monai.Deploy.InformaticsGateway.Services.Connectors;
 using Monai.Deploy.InformaticsGateway.Services.DicomWeb;
 using Monai.Deploy.InformaticsGateway.Services.Export;
+using Monai.Deploy.InformaticsGateway.Services.HealthLevel7;
 using Monai.Deploy.InformaticsGateway.Services.Http;
 using Monai.Deploy.InformaticsGateway.Services.Scp;
 using Monai.Deploy.InformaticsGateway.Services.Storage;
@@ -120,13 +122,16 @@ internal static IHostBuilder CreateHostBuilder(string[] args) =>
                     services.AddSingleton<IMonaiServiceLocator, MonaiServiceLocator>();
                     services.AddSingleton<IStorageInfoProvider, StorageInfoProvider>();
                     services.AddSingleton<IMonaiAeChangedNotificationService, MonaiAeChangedNotificationService>();
+                    services.AddSingleton<ITcpListenerFactory, TcpListenerFactory>();
+                    services.AddSingleton<IMllpClientFactory, MllpClientFactory>();
                     services.AddSingleton<IApplicationEntityManager, ApplicationEntityManager>();
                     services.AddSingleton<SpaceReclaimerService>();
                     services.AddSingleton<ScpService>();
                     services.AddSingleton<ScuExportService>();
                     services.AddSingleton<DicomWebExportService>();
                     services.AddSingleton<DataRetrievalService>();
                     services.AddSingleton<PayloadNotificationService>();
+                    services.AddSingleton<MllpService>();
 
                     var timeout = TimeSpan.FromSeconds(hostContext.Configuration.GetValue("InformaticsGateway:dicomWeb:clientTimeout", DicomWebConfiguration.DefaultClientTimeout));
                     services
@@ -149,6 +154,7 @@ internal static IHostBuilder CreateHostBuilder(string[] args) =>
                     services.AddHostedService<ScuExportService>(p => p.GetService<ScuExportService>());
                     services.AddHostedService<DicomWebExportService>(p => p.GetService<DicomWebExportService>());
                     services.AddHostedService<PayloadNotificationService>(p => p.GetService<PayloadNotificationService>());
+                    services.AddHostedService<MllpService>(p => p.GetService<MllpService>());
                 })
                 .ConfigureWebHostDefaults(webBuilder =>
                 {

src/InformaticsGateway/Services/Common/INetworkStream.cs

@@ -0,0 +1,21 @@
+// SPDX-FileCopyrightText: © 2022 MONAI Consortium
+// SPDX-License-Identifier: Apache License 2.0
+
+using System;
+using System.Threading;
+using System.Threading.Tasks;
+
+namespace Monai.Deploy.InformaticsGateway.Services.Common
+{
+    internal interface INetworkStream : IDisposable
+    {
+        int ReadTimeout { get; set; }
+        int WriteTimeout { get; set; }
+
+        ValueTask WriteAsync(ReadOnlyMemory<byte> ackData, CancellationToken cancellationToken = default);
+
+        Task FlushAsync(CancellationToken cancellationToken = default);
+
+        ValueTask<int> ReadAsync(Memory<byte> messageBuffer, CancellationToken cancellationToken = default);
+    }
+}

src/InformaticsGateway/Services/Common/ITcpClientAdapter.cs

@@ -0,0 +1,15 @@
+// SPDX-FileCopyrightText: © 2022 MONAI Consortium
+// SPDX-License-Identifier: Apache License 2.0
+
+using System;
+using System.Net;
+
+namespace Monai.Deploy.InformaticsGateway.Services.Common
+{
+    internal interface ITcpClientAdapter : IDisposable
+    {
+        EndPoint RemoteEndPoint { get; }
+
+        INetworkStream GetStream();
+    }
+}