Store & notify HL7 messages (#113)

* gh-102 Queue to upload received HL7 messages & notify payload assembler
* gh-102 Update CLI to export HL7 port with Docker
* gh-102 Add new test feature for HL7
* Update license scan settings

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

Author: mocsharp

.github/workflows/ci.yml

@@ -45,6 +45,10 @@ jobs:
         with:
           fetch-depth: 0
 
+      - uses: actions/setup-dotnet@v1
+        with:
+          dotnet-version: "6.0.x"
+          
       - name: Install GitVersion
         run: dotnet tool install --global GitVersion.Tool
 
@@ -199,7 +203,7 @@ jobs:
     needs: [build]
     strategy:
       matrix:
-        feature: [AcrApi, DicomDimseScp, DicomDimseScu, DicomWebExport, DicomWebStow]
+        feature: [AcrApi, DicomDimseScp, DicomDimseScu, DicomWebExport, DicomWebStow, HealthLevel7]
       fail-fast: false
     env:
       TAG: ${{ needs.build.outputs.TAG }}

.licenserc.yaml

@@ -28,6 +28,8 @@ header:
     - '**/*.feature.cs'
     - 'src/.sonarlint/**'
     - 'src/coverlet.runsettings'
+    - 'src/Monai.Deploy.InformaticsGateway.sln'
+    - 'src/Database/Migrations/**'
     - 'demos/**/.env/**'
     - 'docs/templates/**'
     - 'tests/Integration.Test/*.dev'

Dockerfile

@@ -45,6 +45,7 @@ COPY --from=build /app/out .
 COPY --from=build /tools /opt/dotnetcore-tools
 
 EXPOSE 104
+EXPOSE 2575
 EXPOSE 5000
 
 RUN ls -lR /opt/monai/ig

global.json

@@ -1,6 +1,6 @@
 {
   "sdk": {
-    "version": "6.0.100",
+    "version": "6.0.400",
     "rollForward": "latestFeature"
   }
 }

src/Api/Storage/Hl7FileStorageMetadata.cs

@@ -0,0 +1,63 @@
+/*
+ * Copyright 2021-2022 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.
+ */
+
+using System;
+using System.Text.Json.Serialization;
+using Ardalis.GuardClauses;
+
+namespace Monai.Deploy.InformaticsGateway.Api.Storage
+{
+    /// <summary>
+    /// Provides basic information for a FHIR resource and storage hierarchy/path.
+    /// </summary>
+    public sealed record Hl7FileStorageMetadata : FileStorageMetadata
+    {
+        public const string Hl7SubDirectoryName = "ehr";
+        public const string FileExtension = ".txt";
+
+        /// <inheritdoc/>
+        [JsonIgnore]
+        public override string DataTypeDirectoryName => Hl7SubDirectoryName;
+
+        /// <inheritdoc/>
+        [JsonPropertyName("file")]
+        public override StorageObjectMetadata File { get; set; }
+
+        /// <summary>
+        /// DO NOT USE
+        /// This constructor is intended for JSON serializer.
+        /// Due to limitation in current version of .NET, the constructor must be public.
+        /// https://github.com/dotnet/runtime/issues/31511
+        /// </summary>
+        [JsonConstructor]
+        public Hl7FileStorageMetadata() { }
+
+        public Hl7FileStorageMetadata(string connectionId)
+            : base(connectionId, Guid.NewGuid().ToString())
+        {
+            Guard.Against.NullOrWhiteSpace(connectionId, nameof(connectionId));
+
+            Source = connectionId;
+
+            File = new StorageObjectMetadata(FileExtension)
+            {
+                TemporaryPath = string.Join(PathSeparator, connectionId, DataTypeDirectoryName, $"{base.Id}{FileExtension}"),
+                UploadPath = string.Join(PathSeparator, DataTypeDirectoryName, $"{base.Id}{FileExtension}"),
+                ContentType = System.Net.Mime.MediaTypeNames.Text.Plain,
+            };
+        }
+    }
+}

src/Api/Test/Storage/StorageObjectMetadataTest.cs

@@ -34,8 +34,10 @@ public void GivenAStorageObjectMetadata_InitializeWithFileExtensionMissingDot_Ex
         [Fact]
         public void GivenAStorageObjectMetadata_WhenSetUploadIsCalled_ExpectUplaodValuesToBeSetAndDataStreamDisposed()
         {
-            var metadata = new StorageObjectMetadata(".txt");
-            metadata.Data = new MemoryStream();
+            var metadata = new StorageObjectMetadata(".txt")
+            {
+                Data = new MemoryStream()
+            };
             metadata.SetUploaded("MYBUCKET");
 
             Assert.Equal("MYBUCKET", metadata.TemporaryBucketName);

src/CLI/Services/ConfigurationOptionAccessor.cs

@@ -30,6 +30,11 @@ public interface IConfigurationOptionAccessor
         /// </summary>
         int DicomListeningPort { get; set; }
 
+        /// <summary>
+        /// Gets or sets the HL7 listening port from appsettings.json.
+        /// </summary>
+        int Hl7ListeningPort { get; set; }
+
         /// <summary>
         /// Gets or sets the Docker image prefix from appsettings.json.
         /// This is used to query the Informatics Gateway Docker containers that are installed.
@@ -105,13 +110,28 @@ public int DicomListeningPort
             }
             set
             {
-                Guard.Against.OutOfRangePort(value, nameof(InformaticsGatewayServerEndpoint));
+                Guard.Against.OutOfRangePort(value, nameof(DicomListeningPort));
                 var jObject = ReadConfigurationFile();
                 jObject["InformaticsGateway"]["dicom"]["scp"]["port"] = value;
                 SaveConfigurationFile(jObject);
             }
         }
 
+        public int Hl7ListeningPort
+        {
+            get
+            {
+                return GetValueFromJsonPath<int>("InformaticsGateway.hl7.port");
+            }
+            set
+            {
+                Guard.Against.OutOfRangePort(value, nameof(Hl7ListeningPort));
+                var jObject = ReadConfigurationFile();
+                jObject["InformaticsGateway"]["hl7"]["port"] = value;
+                SaveConfigurationFile(jObject);
+            }
+        }
+
         public string DockerImagePrefix
         {
             get

src/CLI/Services/DockerRunner.cs

@@ -119,6 +119,10 @@ public async Task<bool> StartApplication(ImageVersion imageVersion, Cancellation
             createContainerParams.ExposedPorts.Add($"{_configurationService.Configurations.DicomListeningPort}/tcp", new EmptyStruct());
             createContainerParams.HostConfig.PortBindings.Add($"{_configurationService.Configurations.DicomListeningPort}/tcp", new List<PortBinding> { new PortBinding { HostPort = $"{_configurationService.Configurations.DicomListeningPort}" } });
 
+            _logger.DockerPrtBinding(_configurationService.Configurations.Hl7ListeningPort);
+            createContainerParams.ExposedPorts.Add($"{_configurationService.Configurations.Hl7ListeningPort}/tcp", new EmptyStruct());
+            createContainerParams.HostConfig.PortBindings.Add($"{_configurationService.Configurations.Hl7ListeningPort}/tcp", new List<PortBinding> { new PortBinding { HostPort = $"{_configurationService.Configurations.Hl7ListeningPort}" } });
+
             _logger.DockerPrtBinding(_configurationService.Configurations.InformaticsGatewayServerPort);
             createContainerParams.ExposedPorts.Add($"{_configurationService.Configurations.InformaticsGatewayServerPort}/tcp", new EmptyStruct());
             createContainerParams.HostConfig.PortBindings.Add($"{_configurationService.Configurations.InformaticsGatewayServerPort}/tcp", new List<PortBinding> { new PortBinding { HostPort = $"{_configurationService.Configurations.InformaticsGatewayServerPort}" } });

src/Client.Common/Monai.Deploy.InformaticsGateway.Client.Common.csproj

@@ -17,7 +17,7 @@
 <Project Sdk="Microsoft.NET.Sdk">
 
   <PropertyGroup>
-    <TargetFramework>netstandard2.1</TargetFramework>
+    <TargetFramework>net6.0</TargetFramework>
     <RootNamespace>Monai.Deploy.InformaticsGateway.Client.Common</RootNamespace>
     <PackageLicenseExpression>Apache-2.0</PackageLicenseExpression>
     <IsTrimmable>true</IsTrimmable>

src/Common/Monai.Deploy.InformaticsGateway.Common.csproj

@@ -19,7 +19,7 @@
 
   <PropertyGroup>
     <RootNamespace>Monai.Deploy.InformaticsGateway.Common</RootNamespace>
-    <TargetFramework>netstandard2.1</TargetFramework>
+    <TargetFramework>net6.0</TargetFramework>
     <PackageLicenseExpression>Apache-2.0</PackageLicenseExpression>
     <IsTrimmable>true</IsTrimmable>
     <ProduceReferenceAssembly>True</ProduceReferenceAssembly>

src/Configuration/Hl7Configuration.cs

@@ -1,17 +1,31 @@
-// SPDX-FileCopyrightText: © 2022 MONAI Consortium
-// SPDX-License-Identifier: Apache License 2.0
+/*
+ * 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.
+ */
 
 using Microsoft.Extensions.Configuration;
 
 namespace Monai.Deploy.InformaticsGateway.Configuration
 {
     public class Hl7Configuration
     {
-        public static readonly int DefaultClientTimeout = 300000;
+        public static readonly int DefaultClientTimeout = 60000;
         public const int DefaultMaximumNumberOfConnections = 10;
 
         /// <summary>
         /// Gets or sets the client connection timeout in milliseconds.
+        /// Defaults to 60,000ms.
         /// </summary>
         [ConfigurationKeyName("clientTimeout")]
         public int ClientTimeoutMilliseconds { get; set; } = DefaultClientTimeout;
@@ -27,7 +41,7 @@ public class Hl7Configuration
         /// Gets or sets the MLLP listening port.
         /// Defaults to 2575.
         /// </summary>
-        [ConfigurationKeyName("clientTimeout")]
+        [ConfigurationKeyName("port")]
         public int Port { get; set; } = 2575;
 
         /// <summary>

src/Database/Migrations/20220802200605_R3_0.3.0.Designer.cs

@@ -1,4 +1,20 @@
-using Microsoft.EntityFrameworkCore.Migrations;
+/*
+ * 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.
+ */
+
+using Microsoft.EntityFrameworkCore.Migrations;
 
 #nullable disable
 

src/Database/Migrations/20220802200605_R3_0.3.0.cs

@@ -1,4 +1,20 @@
-// <auto-generated />
+/*
+ * 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.
+ */
+
+// <auto-generated />
 using System;
 using Microsoft.EntityFrameworkCore;
 using Microsoft.EntityFrameworkCore.Infrastructure;

src/Database/Migrations/InformaticsGatewayContextModelSnapshot.cs

@@ -15,32 +15,15 @@
  * limitations under the License.
  */
 
-using System;
-using System.Collections.Generic;
-using System.Linq;
-using System.Text.Json;
-using System.Text.Json.Serialization;
 using Microsoft.EntityFrameworkCore;
-using Microsoft.EntityFrameworkCore.ChangeTracking;
 using Microsoft.EntityFrameworkCore.Metadata.Builders;
-using Monai.Deploy.InformaticsGateway.Api.Storage;
 
 namespace Monai.Deploy.InformaticsGateway.Database
 {
     internal class StorageMetadataWrapperEntityConfiguration : IEntityTypeConfiguration<StorageMetadataWrapper>
     {
         public void Configure(EntityTypeBuilder<StorageMetadataWrapper> builder)
         {
-            var filesComparer = new ValueComparer<IList<FileStorageMetadata>>(
-                (c1, c2) => c1.SequenceEqual(c2),
-                c => c.Aggregate(0, (a, v) => HashCode.Combine(a, v.GetHashCode())),
-                c => c.ToList());
-
-            var jsonSerializerSettings = new JsonSerializerOptions
-            {
-                DefaultIgnoreCondition = JsonIgnoreCondition.WhenWritingNull
-            };
-
             builder.HasKey(j => new
             {
                 j.CorrelationId,

src/Database/StorageMetadataWrapperEntityConfiguration.cs

@@ -1,3 +1,19 @@
+<!--
+  ~ 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.
+-->
+
 <Project Sdk="Microsoft.NET.Sdk">
 
   <PropertyGroup>

src/Database/Test/Monai.Deploy.InformaticsGateway.Database.Test.csproj

@@ -1 +1,17 @@
+/*
+ * 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.
+ */
+
 global using Xunit;

src/Database/Test/Usings.cs

@@ -74,8 +74,9 @@ public interface IDicomWebClient
         /// </summary>
         /// <param name="serviceType"><c>ServiceType</c> to be configured</param>
         /// <param name="urlPrefix">Url prefix</param>
+        #pragma warning disable CA1054
         void ConfigureServicePrefix(DicomWebServiceType serviceType, string urlPrefix);
-
+        #pragma warning restore CA1054
         /// <summary>
         /// Configures the authentication header for the DICOMweb client.
         /// </summary>

src/DicomWebClient/API/IDicomWebClient.cs

@@ -19,6 +19,8 @@ namespace Monai.Deploy.InformaticsGateway.DicomWeb.Client.API
 {
     public interface IServiceBase
     {
+        #pragma warning disable CA1054
         bool TryConfigureServiceUriPrefix(string uriPrefix);
+        #pragma warning restore CA1054
     }
 }