Update fo-dicom to 5.0.3 (#164)

* Update fo-dicom to 5.0.3 and handle breaking changes
* Make validation on DICOM to JSON serialization configurable

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

Author: mocsharp

doc/dependency_decisions.yml

@@ -804,6 +804,13 @@
     :versions:
     - 17.3.1
     :when: 2022-09-01 23:06:18.619013325 Z
+- - :approve
+  - Microsoft.Toolkit.HighPerformance
+  - :who: mocsharp
+    :why: MIT (https://github.com/CommunityToolkit/WindowsCommunityToolkit/raw/main/License.md)
+    :versions:
+    - 7.1.2
+    :when: 2022-09-20 00:42:18.619013325 Z
 - - :approve
   - Microsoft.Win32.Primitives
   - :who: mocsharp
@@ -1866,7 +1873,7 @@
   - :who: mocsharp
     :why: Microsoft Public License (https://github.com/fo-dicom/fo-dicom/raw/development/License.txt)
     :versions:
-    - 5.0.2
+    - 5.0.3
     :when: 2022-08-16 23:07:29.574869349 Z
 - - :approve
   - runtime.any.System.Collections
@@ -2400,4 +2407,3 @@
     :versions:
     - 4.0.1
     :when: 2022-08-16 23:10:21.184627612 Z
-    

docker-compose/docker-compose.dev.yml

@@ -39,7 +39,8 @@ services:
       - ./.run/minio/data:/data
       - ./.run/minio/config:/root/.minio
     ports:
-      - "9000:9000"
+      - 9000:9000
+      - 9001:9001
     environment:
       MINIO_ROOT_USER: minioadmin
       MINIO_ROOT_PASSWORD: minioadmin

docs/compliance/third-party-licenses.md

@@ -6045,6 +6045,41 @@ SOFTWARE.
 </details>
 
 
+<details>
+<summary>Microsoft.Toolkit.HighPerformance 7.1.2</summary>
+
+## Microsoft.Toolkit.HighPerformance
+
+- Version: 7.1.2
+- Authors: Microsoft
+- Owners: Microsoft.Toolkit,dotnetfoundation
+- Project URL: https://dot.net/
+- Source: [NuGet](https://www.nuget.org/packages/Microsoft.Toolkit.HighPerformance/7.1.2)
+- License: [MIT]( https://github.com/CommunityToolkit/WindowsCommunityToolkit/raw/main/License.md)
+
+
+```
+# Windows Community Toolkit
+
+Copyright © .NET Foundation and Contributors
+
+All rights reserved.
+
+## MIT License (MIT)
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”),
+to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense,
+and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED *AS IS*, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS
+IN THE SOFTWARE.
+```
+
+</details>
 <details>
 <summary>Microsoft.Win32.Primitives 4.3.0</summary>
 
@@ -26864,14 +26899,14 @@ SOFTWARE.
 
 
 <details>
-<summary>fo-dicom 5.0.2</summary>
+<summary>fo-dicom 5.0.3</summary>
 
 ## fo-dicom
 
-- Version: 5.0.2
+- Version: 5.0.3
 - Authors: fo-dicom contributors
 - Project URL: https://github.com/fo-dicom/fo-dicom
-- Source: [NuGet](https://www.nuget.org/packages/fo-dicom/5.0.2)
+- Source: [NuGet](https://www.nuget.org/packages/fo-dicom/5.0.3)
 - License: [Microsoft Public License](https://github.com/fo-dicom/fo-dicom/raw/development/License.txt)
 
 
@@ -39929,4 +39964,4 @@ The above copyright notice and this permission notice (including the next paragr
 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL _____ BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 ```
 
-</details>
+</details>

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

@@ -28,7 +28,7 @@
 
   <ItemGroup>
     <PackageReference Include="Ardalis.GuardClauses" Version="4.0.1" />
-    <PackageReference Include="fo-dicom" Version="5.0.2" />
+    <PackageReference Include="fo-dicom" Version="5.0.3" />
     <PackageReference Include="GitVersion.MsBuild" Version="5.10.3">
       <PrivateAssets>All</PrivateAssets>
     </PackageReference>

src/Configuration/DicomConfiguration.cs

@@ -41,5 +41,11 @@ public class DicomConfiguration
         /// </summary>
         [ConfigurationKeyName("writeDicomJson")]
         public DicomJsonOptions WriteDicomJson { get; set; } = DicomJsonOptions.IgnoreOthers;
+
+        /// <summary>
+        /// Gets or sets whether to automatically validate the DICOM values when serializing to JSON.
+        /// Defaults to False.
+        /// </summary>
+        public bool ValidateDicomOnSerialization { get; set; } = false;
     }
 }

src/DicomWebClient/CLI/Monai.Deploy.InformaticsGateway.DicomWeb.Client.CLI.csproj

@@ -35,7 +35,7 @@
 
   <ItemGroup>
     <PackageReference Include="ConsoleAppFramework" Version="4.2.2" />
-    <PackageReference Include="fo-dicom" Version="5.0.2" />
+    <PackageReference Include="fo-dicom" Version="5.0.3" />
     <PackageReference Include="Microsoft.Extensions.Http" Version="6.0.0" />
   </ItemGroup>
 </Project>

src/DicomWebClient/Monai.Deploy.InformaticsGateway.DicomWeb.Client.csproj

@@ -43,7 +43,7 @@
 
   <ItemGroup>
     <PackageReference Include="Ardalis.GuardClauses" Version="4.0.1" />
-    <PackageReference Include="fo-dicom" Version="5.0.2" />
+    <PackageReference Include="fo-dicom" Version="5.0.3" />
     <PackageReference Include="GitVersion.MsBuild" Version="5.10.3">
       <PrivateAssets>All</PrivateAssets>
     </PackageReference>

src/InformaticsGateway/Common/DicomExtensions.cs

@@ -52,12 +52,15 @@ public static DicomTransferSyntax[] ToDicomTransferSyntaxArray(this IEnumerable<
             return dicomTransferSyntaxes.ToArray();
         }
 
-        public static string ToJson(this DicomFile dicomFile, DicomJsonOptions dicomJsonOptions)
+        public static string ToJson(this DicomFile dicomFile, DicomJsonOptions dicomJsonOptions, bool validateDicom)
         {
             Guard.Against.Null(dicomFile, nameof(dicomFile));
 
             var options = new JsonSerializerOptions();
-            options.Converters.Add(new DicomJsonConverter(writeTagsAsKeywords: false, autoValidate: true));
+            options.Converters.Add(new DicomJsonConverter(
+                writeTagsAsKeywords: false,
+                autoValidate: validateDicom,
+                numberSerializationMode: validateDicom ? NumberSerializationMode.AsNumber : NumberSerializationMode.PreferablyAsNumber));
             options.WriteIndented = false;
 
             if (dicomJsonOptions == DicomJsonOptions.Complete)

src/InformaticsGateway/Monai.Deploy.InformaticsGateway.csproj

@@ -34,7 +34,7 @@
   <ItemGroup>
     <PackageReference Include="Ardalis.GuardClauses" Version="4.0.1" />
     <PackageReference Include="DotNext.Threading" Version="4.7.1" />
-    <PackageReference Include="fo-dicom" Version="5.0.2" />
+    <PackageReference Include="fo-dicom" Version="5.0.3" />
     <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">

src/InformaticsGateway/Services/Connectors/DataRetrievalService.cs

@@ -509,7 +509,7 @@ private async Task RetrieveInstances(string transactionId, IDicomWebClient dicom
                     }
 
                     var dicomFileStorageMetadata = SaveFile(transactionId, file, uids);
-                    await dicomFileStorageMetadata.SetDataStreams(file, file.ToJson(_options.Value.Dicom.WriteDicomJson)).ConfigureAwait(false);
+                    await dicomFileStorageMetadata.SetDataStreams(file, file.ToJson(_options.Value.Dicom.WriteDicomJson, _options.Value.Dicom.ValidateDicomOnSerialization)).ConfigureAwait(false);
                     retrievedInstance.Add(uids.Identifier, dicomFileStorageMetadata);
                     count++;
                 }
@@ -539,7 +539,7 @@ private async Task SaveFiles(string transactionId, IAsyncEnumerable<DicomFile> f
                 }
 
                 var dicomFileStorageMetadata = SaveFile(transactionId, file, uids);
-                await dicomFileStorageMetadata.SetDataStreams(file, file.ToJson(_options.Value.Dicom.WriteDicomJson)).ConfigureAwait(false);
+                await dicomFileStorageMetadata.SetDataStreams(file, file.ToJson(_options.Value.Dicom.WriteDicomJson, _options.Value.Dicom.ValidateDicomOnSerialization)).ConfigureAwait(false);
                 retrievedInstance.Add(uids.Identifier, dicomFileStorageMetadata);
             }
         }

src/InformaticsGateway/Services/DicomWeb/IStreamsWriter.cs

@@ -165,7 +165,7 @@ private async Task SaveInstance(Stream stream, string studyInstanceUid, string w
                 dicomInfo.SetWorkflows(workflowName);
             }
 
-            await dicomInfo.SetDataStreams(dicomFile, dicomFile.ToJson(_configuration.Value.Dicom.WriteDicomJson)).ConfigureAwait(false);
+            await dicomInfo.SetDataStreams(dicomFile, dicomFile.ToJson(_configuration.Value.Dicom.WriteDicomJson, _configuration.Value.Dicom.ValidateDicomOnSerialization)).ConfigureAwait(false);
             _uploadQueue.Queue(dicomInfo);
 
             // for DICOMweb, use correlation ID as the grouping key

src/InformaticsGateway/Services/Export/ScuExportService.cs

@@ -78,7 +78,6 @@ private async Task HandleDesination(ExportRequestDataMessage exportRequestData,
             Guard.Against.Null(exportRequestData, nameof(exportRequestData));
 
             var manualResetEvent = new ManualResetEvent(false);
-            IDicomClient client = null;
             DestinationApplicationEntity destination = null;
             try
             {
@@ -93,38 +92,38 @@ private async Task HandleDesination(ExportRequestDataMessage exportRequestData,
 
             try
             {
-                client = DicomClientFactory.Create(
-                    destination.HostIp,
-                    destination.Port,
-                    false,
-                    _configuration.Value.Dicom.Scu.AeTitle,
-                    destination.AeTitle);
-
-                client.AssociationAccepted += (sender, args) => _logger.AssociationAccepted();
-                client.AssociationRejected += (sender, args) => _logger.AssociationRejected();
-                client.AssociationReleased += (sender, args) => _logger.AssociationReleased();
-                client.ServiceOptions.LogDataPDUs = _configuration.Value.Dicom.Scu.LogDataPdus;
-                client.ServiceOptions.LogDimseDatasets = _configuration.Value.Dicom.Scu.LogDimseDatasets;
-
-                client.NegotiateAsyncOps();
-                if (GenerateRequests(exportRequestData, client, manualResetEvent))
-                {
-                    await Policy
-                       .Handle<Exception>()
-                       .WaitAndRetryAsync(
-                           _configuration.Value.Export.Retries.RetryDelays,
-                           (exception, timeSpan, retryCount, context) =>
-                           {
-                               _logger.DimseExportErrorWithRetry(timeSpan, retryCount, exception);
-                           })
-                       .ExecuteAsync(async () =>
+                await Policy
+                   .Handle<Exception>()
+                   .WaitAndRetryAsync(
+                       _configuration.Value.Export.Retries.RetryDelays,
+                       (exception, timeSpan, retryCount, context) =>
+                       {
+                           _logger.DimseExportErrorWithRetry(timeSpan, retryCount, exception);
+                       })
+                   .ExecuteAsync(async () =>
+                   {
+                       var client = DicomClientFactory.Create(
+                               destination.HostIp,
+                               destination.Port,
+                               false,
+                               _configuration.Value.Dicom.Scu.AeTitle,
+                               destination.AeTitle);
+
+                       client.AssociationAccepted += (sender, args) => _logger.AssociationAccepted();
+                       client.AssociationRejected += (sender, args) => _logger.AssociationRejected();
+                       client.AssociationReleased += (sender, args) => _logger.AssociationReleased();
+                       client.ServiceOptions.LogDataPDUs = _configuration.Value.Dicom.Scu.LogDataPdus;
+                       client.ServiceOptions.LogDimseDatasets = _configuration.Value.Dicom.Scu.LogDimseDatasets;
+
+                       client.NegotiateAsyncOps();
+                       if (await GenerateRequestsAsync(exportRequestData, client, manualResetEvent))
                        {
                            _logger.DimseExporting(destination.AeTitle, destination.HostIp, destination.Port);
                            await client.SendAsync(cancellationToken).ConfigureAwait(false);
                            manualResetEvent.WaitOne();
                            _logger.DimseExportComplete(destination.AeTitle);
-                       }).ConfigureAwait(false);
-                }
+                       }
+                   }).ConfigureAwait(false);
             }
             catch (Exception ex)
             {
@@ -151,7 +150,7 @@ private DestinationApplicationEntity LookupDestination(string destinationName)
             return destination;
         }
 
-        private bool GenerateRequests(
+        private async Task<bool> GenerateRequestsAsync(
             ExportRequestDataMessage exportRequestData,
             IDicomClient client,
             ManualResetEvent manualResetEvent)
@@ -177,7 +176,7 @@ private bool GenerateRequests(
                     manualResetEvent.Set();
                 };
 
-                client.AddRequestAsync(request).ConfigureAwait(false);
+                await client.AddRequestAsync(request).ConfigureAwait(false);
                 return true;
             }
             catch (Exception exception)

src/InformaticsGateway/Services/Scp/ApplicationEntityHandler.cs

@@ -41,6 +41,7 @@ internal class ApplicationEntityHandler : IDisposable, IApplicationEntityHandler
 
         private MonaiApplicationEntity _configuration;
         private DicomJsonOptions _dicomJsonOptions;
+        private bool _validateDicomValueOnJsonSerialization;
         private bool _disposedValue;
 
         public ApplicationEntityHandler(
@@ -55,12 +56,13 @@ public ApplicationEntityHandler(
             _uploadQueue = _serviceScope.ServiceProvider.GetService<IObjectUploadQueue>() ?? throw new ServiceNotFoundException(nameof(IObjectUploadQueue));
         }
 
-        public void Configure(MonaiApplicationEntity monaiApplicationEntity, DicomJsonOptions dicomJsonOptions)
+        public void Configure(MonaiApplicationEntity monaiApplicationEntity, DicomJsonOptions dicomJsonOptions, bool validateDicomValuesOnJsonSerialization)
         {
             Guard.Against.Null(monaiApplicationEntity, nameof(monaiApplicationEntity));
 
             _configuration = monaiApplicationEntity;
             _dicomJsonOptions = dicomJsonOptions;
+            _validateDicomValueOnJsonSerialization = validateDicomValuesOnJsonSerialization;
         }
 
         public async Task HandleInstanceAsync(DicomCStoreRequest request, string calledAeTitle, string callingAeTitle, Guid associationId, StudySerieSopUids uids)
@@ -93,7 +95,7 @@ public async Task HandleInstanceAsync(DicomCStoreRequest request, string calledA
                 dicomInfo.SetWorkflows(_configuration.Workflows.ToArray());
             }
 
-            await dicomInfo.SetDataStreams(request.File, request.File.ToJson(_dicomJsonOptions)).ConfigureAwait(false);
+            await dicomInfo.SetDataStreams(request.File, request.File.ToJson(_dicomJsonOptions, _validateDicomValueOnJsonSerialization)).ConfigureAwait(false);
             _uploadQueue.Queue(dicomInfo);
 
             var dicomTag = FellowOakDicom.DicomTag.Parse(_configuration.Grouping);

src/InformaticsGateway/Services/Scp/ApplicationEntityManager.cs

@@ -143,7 +143,7 @@ private void AddNewAeTitle(MonaiApplicationEntity entity)
         {
             var scope = _serviceScopeFactory.CreateScope();
             var handler = scope.ServiceProvider.GetService<IApplicationEntityHandler>() ?? throw new ServiceNotFoundException(nameof(IApplicationEntityHandler));
-            handler.Configure(entity, Configuration.Value.Dicom.WriteDicomJson);
+            handler.Configure(entity, Configuration.Value.Dicom.WriteDicomJson, Configuration.Value.Dicom.ValidateDicomOnSerialization);
 
             if (!_aeTitles.TryAdd(entity.AeTitle, handler))
             {

src/InformaticsGateway/Services/Scp/IApplicationEntityHandler.cs

@@ -25,7 +25,7 @@ namespace Monai.Deploy.InformaticsGateway.Services.Scp
 {
     internal interface IApplicationEntityHandler
     {
-        void Configure(MonaiApplicationEntity monaiApplicationEntity, DicomJsonOptions dicomJsonOptions);
+        void Configure(MonaiApplicationEntity monaiApplicationEntity, DicomJsonOptions dicomJsonOptions, bool validateDicomValuesOnJsonSerialization);
 
         Task HandleInstanceAsync(DicomCStoreRequest request, string calledAeTitle, string callingAeTitle, Guid associationId, StudySerieSopUids uids);
     }

src/InformaticsGateway/Services/Scp/ScpServiceInternal.cs

@@ -21,8 +21,6 @@
 using System.Threading;
 using System.Threading.Tasks;
 using FellowOakDicom;
-using FellowOakDicom.Imaging.Codec;
-using FellowOakDicom.Log;
 using FellowOakDicom.Network;
 using Monai.Deploy.InformaticsGateway.Api;
 using Monai.Deploy.InformaticsGateway.Common;
@@ -44,8 +42,8 @@ internal class ScpServiceInternal :
         private IDisposable _loggerScope;
         private Guid _associationId;
 
-        public ScpServiceInternal(INetworkStream stream, Encoding fallbackEncoding, FellowOakDicom.Log.ILogger log, ILogManager logManager, INetworkManager network, ITranscoderManager transcoder)
-                : base(stream, fallbackEncoding, log, logManager, network, transcoder)
+        public ScpServiceInternal(INetworkStream stream, Encoding fallbackEncoding, FellowOakDicom.Log.ILogger log, DicomServiceDependencies dicomServiceDependencies)
+                : base(stream, fallbackEncoding, log, dicomServiceDependencies)
         {
         }