HL7 improve logging

Signed-off-by: Neil South <neil.south@answerdigital.com>

.github/workflows/ci.yml

@@ -183,11 +183,11 @@ jobs:
         ports:
         - 27017:27017
     steps:
-      - name: Set up JDK 11
+      - name: Set up JDK 17
         uses: actions/setup-java@v3
         with:
           distribution: zulu
-          java-version: '11'
+          java-version: '17'
 
       - uses: actions/setup-dotnet@v3
         with:

src/Api/Hl7ApplicationConfigEntity.cs

@@ -26,7 +26,7 @@
 
 namespace Monai.Deploy.InformaticsGateway.Api
 {
-    public class Hl7ApplicationConfigEntity : MongoDBEntityBase
+    public sealed class Hl7ApplicationConfigEntity : MongoDBEntityBase
     {
         /// <summary>
         /// Gets or sets the name of a Hl7 application entity.
@@ -60,6 +60,8 @@ public class Hl7ApplicationConfigEntity : MongoDBEntityBase
         /// </summary>
         public List<string> PlugInAssemblies { get; set; } = default!;
 
+        public DateTime LastModified { get; set; } = DateTime.UtcNow;
+
         public IEnumerable<string> Validate()
         {
             var errors = new List<string>();
@@ -114,7 +116,7 @@ public override string ToString()
     }
 
     //string key, string value
-    public class StringKeyValuePair : IKeyValuePair<string, string>
+    public sealed class StringKeyValuePair : IKeyValuePair<string, string>, IEquatable<StringKeyValuePair>
     {
         [Key]
         public string Key { get; set; } = string.Empty;
@@ -136,7 +138,7 @@ public static List<StringKeyValuePair> FromDictionary(Dictionary<string, string>
 
     }
 
-    public class DataKeyValuePair : IKeyValuePair<string, DataLinkType>
+    public sealed class DataKeyValuePair : IKeyValuePair<string, DataLinkType>, IEquatable<DataKeyValuePair>
     {
         [Key]
         public string Key { get; set; } = string.Empty;

src/InformaticsGateway/Services/HealthLevel7/IMllpClient.cs → src/Api/Mllp/IMllpClient.cs

@@ -18,14 +18,14 @@
 using System.Threading;
 using System.Threading.Tasks;
 
-namespace Monai.Deploy.InformaticsGateway.Services.HealthLevel7
+namespace Monai.Deploy.InformaticsGateway.Api.Mllp
 {
-    internal interface IMllpClient : IDisposable
+    public interface IMllpClient : IDisposable
     {
         Guid ClientId { get; }
 
         string ClientIp { get; }
 
         Task Start(Func<IMllpClient, MllpClientResult, Task> onDisconnect, CancellationToken cancellationToken);
     }
-}
+}

src/InformaticsGateway/Services/HealthLevel7/IMllpExtract.cs → src/Api/Mllp/IMllpExtract.cs

@@ -19,10 +19,12 @@
 using HL7.Dotnetcore;
 using Monai.Deploy.InformaticsGateway.Api.Storage;
 
-namespace Monai.Deploy.InformaticsGateway.Services.HealthLevel7
+namespace Monai.Deploy.InformaticsGateway.Api.Mllp
 {
-    internal interface IMllpExtract
+    public interface IMllpExtract
     {
-        Task<Message> ExtractInfo(Hl7FileStorageMetadata meta, Message message);
+        Task<Message> ExtractInfo(Hl7FileStorageMetadata meta, Message message, Hl7ApplicationConfigEntity configItem);
+
+        Task<Hl7ApplicationConfigEntity?> GetConfigItem(Message message);
     }
 }

src/InformaticsGateway/Services/HealthLevel7/IMllpService.cs → src/Api/Mllp/IMllpService.cs

@@ -18,7 +18,7 @@
 using System.Threading;
 using System.Threading.Tasks;
 
-namespace Monai.Deploy.InformaticsGateway.Services.HealthLevel7
+namespace Monai.Deploy.InformaticsGateway.Api.Mllp
 {
     public interface IMllpService
     {

src/InformaticsGateway/Services/HealthLevel7/MllpClientResult.cs → src/Api/Mllp/MllpClientResult.cs

@@ -18,9 +18,9 @@
 using System.Collections.Generic;
 using HL7.Dotnetcore;
 
-namespace Monai.Deploy.InformaticsGateway.Services.HealthLevel7
+namespace Monai.Deploy.InformaticsGateway.Api.Mllp
 {
-    internal class MllpClientResult
+    public class MllpClientResult
     {
         public IList<Message> Messages { get; }
         public AggregateException? AggregateException { get; }

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

@@ -53,6 +53,7 @@
 
   <ItemGroup>
     <PackageReference Include="fo-dicom" Version="5.1.1" />
+    <PackageReference Include="HL7-dotnetcore" Version="2.36.0" />
     <PackageReference Include="Macross.Json.Extensions" Version="3.0.0" />
     <PackageReference Include="Microsoft.EntityFrameworkCore.Abstractions" Version="6.0.25" />
     <PackageReference Include="Monai.Deploy.Messaging" Version="1.0.5" />

src/Api/PlugIns/IInputHL7DataPlugIn.cs

@@ -0,0 +1,35 @@
+/*
+ * Copyright 2023 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.Threading.Tasks;
+using HL7.Dotnetcore;
+using Monai.Deploy.InformaticsGateway.Api.Storage;
+
+namespace Monai.Deploy.InformaticsGateway.Api.PlugIns
+{
+    /// <summary>
+    /// <c>IInputDataPlugIn</c> enables lightweight data processing over incoming data received from supported data ingestion
+    /// services.
+    /// Refer to <see cref="IInputHL7DataPlugInEngine" /> for additional details.
+    /// </summary>
+    public interface IInputHL7DataPlugIn
+    {
+        string Name { get; }
+
+        Task<(Message hl7Message, FileStorageMetadata fileMetadata)> ExecuteAsync(Message hl7File, FileStorageMetadata fileMetadata);
+    }
+
+}

src/Api/PlugIns/IInputHL7DataPlugInEngine.cs

@@ -0,0 +1,42 @@
+/*
+ * Copyright 2023 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.Collections.Generic;
+using System.Threading.Tasks;
+using HL7.Dotnetcore;
+using Monai.Deploy.InformaticsGateway.Api.Storage;
+
+namespace Monai.Deploy.InformaticsGateway.Api.PlugIns
+{
+    /// <summary>
+    /// <c>IInputDataPlugInEngine</c> processes incoming data receivied from various supported services through
+    /// a list of plug-ins based on <see cref="IInputDataPlugIn"/>.
+    /// Rules:
+    /// <list type="bullet">
+    /// <item>SCP: A list of plug-ins can be configured with each AET, and each plug-in is executed in the order stored, enabling piping of the incoming data before each file is uploaded to the storage service.</item>
+    /// <item>Incoming data is processed one file at a time and SHALL not wait for the entire study to arrive.</item>
+    /// <item>Plug-ins MUST be lightweight and not hinder the upload process.</item>
+    /// <item>Plug-ins SHALL not accumulate files in memory or storage for bulk processing.</item>
+    /// </list>
+    /// </summary>
+    public interface IInputHL7DataPlugInEngine
+    {
+        void Configure(IReadOnlyList<string> pluginAssemblies);
+
+        Task<Tuple<Message, FileStorageMetadata>> ExecutePlugInsAsync(Message hl7File, FileStorageMetadata fileMetadata, Hl7ApplicationConfigEntity configItem);
+    }
+}

src/Api/Test/packages.lock.json

@@ -94,6 +94,11 @@
           "System.Threading.Channels": "6.0.0"
         }
       },
+      "HL7-dotnetcore": {
+        "type": "Transitive",
+        "resolved": "2.36.0",
+        "contentHash": "N1HLMeIqYuY+4O69ItgZJoDBnnpNkK5N2pClceTJ2nFJxsP48iCsA4iz3tm43Yszi4r/vaThoc3UoLBfGP3vKw=="
+      },
       "Macross.Json.Extensions": {
         "type": "Transitive",
         "resolved": "3.0.0",
@@ -1277,6 +1282,7 @@
       "monai.deploy.informaticsgateway.api": {
         "type": "Project",
         "dependencies": {
+          "HL7-dotnetcore": "[2.36.0, )",
           "Macross.Json.Extensions": "[3.0.0, )",
           "Microsoft.EntityFrameworkCore.Abstractions": "[6.0.25, )",
           "Monai.Deploy.InformaticsGateway.Common": "[1.0.0, )",

src/Api/packages.lock.json

@@ -21,6 +21,12 @@
           "System.Threading.Channels": "6.0.0"
         }
       },
+      "HL7-dotnetcore": {
+        "type": "Direct",
+        "requested": "[2.36.0, )",
+        "resolved": "2.36.0",
+        "contentHash": "N1HLMeIqYuY+4O69ItgZJoDBnnpNkK5N2pClceTJ2nFJxsP48iCsA4iz3tm43Yszi4r/vaThoc3UoLBfGP3vKw=="
+      },
       "Macross.Json.Extensions": {
         "type": "Direct",
         "requested": "[3.0.0, )",

src/CLI/Test/packages.lock.json

@@ -137,6 +137,11 @@
           "System.Threading.Channels": "6.0.0"
         }
       },
+      "HL7-dotnetcore": {
+        "type": "Transitive",
+        "resolved": "2.36.0",
+        "contentHash": "N1HLMeIqYuY+4O69ItgZJoDBnnpNkK5N2pClceTJ2nFJxsP48iCsA4iz3tm43Yszi4r/vaThoc3UoLBfGP3vKw=="
+      },
       "Macross.Json.Extensions": {
         "type": "Transitive",
         "resolved": "3.0.0",
@@ -1560,6 +1565,7 @@
       "monai.deploy.informaticsgateway.api": {
         "type": "Project",
         "dependencies": {
+          "HL7-dotnetcore": "[2.36.0, )",
           "Macross.Json.Extensions": "[3.0.0, )",
           "Microsoft.EntityFrameworkCore.Abstractions": "[6.0.25, )",
           "Monai.Deploy.InformaticsGateway.Common": "[1.0.0, )",

src/CLI/packages.lock.json

@@ -93,6 +93,11 @@
           "System.Threading.Channels": "6.0.0"
         }
       },
+      "HL7-dotnetcore": {
+        "type": "Transitive",
+        "resolved": "2.36.0",
+        "contentHash": "N1HLMeIqYuY+4O69ItgZJoDBnnpNkK5N2pClceTJ2nFJxsP48iCsA4iz3tm43Yszi4r/vaThoc3UoLBfGP3vKw=="
+      },
       "Macross.Json.Extensions": {
         "type": "Transitive",
         "resolved": "3.0.0",
@@ -541,6 +546,7 @@
       "monai.deploy.informaticsgateway.api": {
         "type": "Project",
         "dependencies": {
+          "HL7-dotnetcore": "[2.36.0, )",
           "Macross.Json.Extensions": "[3.0.0, )",
           "Microsoft.EntityFrameworkCore.Abstractions": "[6.0.25, )",
           "Monai.Deploy.InformaticsGateway.Common": "[1.0.0, )",

src/Client/Test/packages.lock.json

@@ -1826,6 +1826,7 @@
       "monai.deploy.informaticsgateway.api": {
         "type": "Project",
         "dependencies": {
+          "HL7-dotnetcore": "[2.36.0, )",
           "Macross.Json.Extensions": "[3.0.0, )",
           "Microsoft.EntityFrameworkCore.Abstractions": "[6.0.25, )",
           "Monai.Deploy.InformaticsGateway.Common": "[1.0.0, )",

src/Client/packages.lock.json

@@ -43,6 +43,11 @@
           "System.Threading.Channels": "6.0.0"
         }
       },
+      "HL7-dotnetcore": {
+        "type": "Transitive",
+        "resolved": "2.36.0",
+        "contentHash": "N1HLMeIqYuY+4O69ItgZJoDBnnpNkK5N2pClceTJ2nFJxsP48iCsA4iz3tm43Yszi4r/vaThoc3UoLBfGP3vKw=="
+      },
       "Macross.Json.Extensions": {
         "type": "Transitive",
         "resolved": "3.0.0",
@@ -274,6 +279,7 @@
       "monai.deploy.informaticsgateway.api": {
         "type": "Project",
         "dependencies": {
+          "HL7-dotnetcore": "[2.36.0, )",
           "Macross.Json.Extensions": "[3.0.0, )",
           "Microsoft.EntityFrameworkCore.Abstractions": "[6.0.25, )",
           "Monai.Deploy.InformaticsGateway.Common": "[1.0.0, )",

src/Configuration/Test/packages.lock.json

@@ -102,6 +102,11 @@
           "System.Threading.Channels": "6.0.0"
         }
       },
+      "HL7-dotnetcore": {
+        "type": "Transitive",
+        "resolved": "2.36.0",
+        "contentHash": "N1HLMeIqYuY+4O69ItgZJoDBnnpNkK5N2pClceTJ2nFJxsP48iCsA4iz3tm43Yszi4r/vaThoc3UoLBfGP3vKw=="
+      },
       "Macross.Json.Extensions": {
         "type": "Transitive",
         "resolved": "3.0.0",
@@ -1290,6 +1295,7 @@
       "monai.deploy.informaticsgateway.api": {
         "type": "Project",
         "dependencies": {
+          "HL7-dotnetcore": "[2.36.0, )",
           "Macross.Json.Extensions": "[3.0.0, )",
           "Microsoft.EntityFrameworkCore.Abstractions": "[6.0.25, )",
           "Monai.Deploy.InformaticsGateway.Common": "[1.0.0, )",

src/Configuration/packages.lock.json

@@ -43,6 +43,11 @@
           "System.Threading.Channels": "6.0.0"
         }
       },
+      "HL7-dotnetcore": {
+        "type": "Transitive",
+        "resolved": "2.36.0",
+        "contentHash": "N1HLMeIqYuY+4O69ItgZJoDBnnpNkK5N2pClceTJ2nFJxsP48iCsA4iz3tm43Yszi4r/vaThoc3UoLBfGP3vKw=="
+      },
       "Macross.Json.Extensions": {
         "type": "Transitive",
         "resolved": "3.0.0",
@@ -274,6 +279,7 @@
       "monai.deploy.informaticsgateway.api": {
         "type": "Project",
         "dependencies": {
+          "HL7-dotnetcore": "[2.36.0, )",
           "Macross.Json.Extensions": "[3.0.0, )",
           "Microsoft.EntityFrameworkCore.Abstractions": "[6.0.25, )",
           "Monai.Deploy.InformaticsGateway.Common": "[1.0.0, )",

src/Database/Api/Test/packages.lock.json

@@ -76,6 +76,11 @@
           "System.Threading.Channels": "6.0.0"
         }
       },
+      "HL7-dotnetcore": {
+        "type": "Transitive",
+        "resolved": "2.36.0",
+        "contentHash": "N1HLMeIqYuY+4O69ItgZJoDBnnpNkK5N2pClceTJ2nFJxsP48iCsA4iz3tm43Yszi4r/vaThoc3UoLBfGP3vKw=="
+      },
       "Macross.Json.Extensions": {
         "type": "Transitive",
         "resolved": "3.0.0",
@@ -1264,6 +1269,7 @@
       "monai.deploy.informaticsgateway.api": {
         "type": "Project",
         "dependencies": {
+          "HL7-dotnetcore": "[2.36.0, )",
           "Macross.Json.Extensions": "[3.0.0, )",
           "Microsoft.EntityFrameworkCore.Abstractions": "[6.0.25, )",
           "Monai.Deploy.InformaticsGateway.Common": "[1.0.0, )",

src/Database/Api/packages.lock.json

@@ -49,6 +49,11 @@
           "System.Threading.Channels": "6.0.0"
         }
       },
+      "HL7-dotnetcore": {
+        "type": "Transitive",
+        "resolved": "2.36.0",
+        "contentHash": "N1HLMeIqYuY+4O69ItgZJoDBnnpNkK5N2pClceTJ2nFJxsP48iCsA4iz3tm43Yszi4r/vaThoc3UoLBfGP3vKw=="
+      },
       "Macross.Json.Extensions": {
         "type": "Transitive",
         "resolved": "3.0.0",
@@ -280,6 +285,7 @@
       "monai.deploy.informaticsgateway.api": {
         "type": "Project",
         "dependencies": {
+          "HL7-dotnetcore": "[2.36.0, )",
           "Macross.Json.Extensions": "[3.0.0, )",
           "Microsoft.EntityFrameworkCore.Abstractions": "[6.0.25, )",
           "Monai.Deploy.InformaticsGateway.Common": "[1.0.0, )",

src/Database/DatabaseMigrationManager.cs

@@ -61,7 +61,7 @@ private static Type[] FindMatchingTypesFromAssemblies(Assembly[] assemblies)
             var matchingTypes = new List<Type>();
             foreach (var assembly in assemblies)
             {
-                var types = assembly.ExportedTypes.Where(p => p.IsAssignableFrom(typeof(IDatabaseMigrationManager)));
+                var types = assembly.ExportedTypes.Where(p => p.IsAssignableFrom(typeof(IDatabaseMigrationManager)) && p.Name != nameof(IDatabaseMigrationManager));
                 if (types.Any())
                 {
                     matchingTypes.AddRange(types);

src/Database/EntityFramework/Migrations/20231204113501_Hl7DEstinationAndConfig.cs

@@ -1,4 +1,4 @@
-using System;
+
 using Microsoft.EntityFrameworkCore.Migrations;
 
 #nullable disable