Merge branch 'main' into release/0.5.1

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

Author: mocsharp

.github/workflows/ci.yml

@@ -603,6 +603,21 @@ jobs:
           separator: "/"
           msg: ${{ github.repository }}
 
+      - name: Unzip docs
+        if: ${{ contains(github.ref, 'refs/heads/main') }}
+        run: |
+          mkdir userguide
+          unzip artifacts/mig-docs-${{ env.SEMVER }}.zip -d userguide/
+          ls -lR userguide/
+
+      - name: Deploy Docs
+        uses: peaceiris/actions-gh-pages@v3
+        if: ${{ contains(github.ref, 'refs/heads/main') }}
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: userguide/
+          publish_branch: docs
+
       - name: Install GitReleaseManager
         uses: gittools/actions/gitreleasemanager/[email protected]
         with:

docs/compliance/third-party-licenses.md

@@ -28,4 +28,4 @@ public interface IMllpClient : IDisposable
 
         Task Start(Func<IMllpClient, MllpClientResult, Task> onDisconnect, CancellationToken cancellationToken);
     }
-}
+}

src/Api/Mllp/IMllpClient.cs

@@ -162,4 +162,4 @@ public static string IpAddress()
             return "127.0.0.1";
         }
     }
-}
+}

src/Api/Storage/FileStorageMetadata.cs

@@ -257,11 +257,8 @@
       },
       "System.Diagnostics.DiagnosticSource": {
         "type": "Transitive",
-        "resolved": "6.0.0",
-        "contentHash": "frQDfv0rl209cKm1lnwTgFPzNigy2EKk1BS3uAvHvlBVKe5cymGyHO+Sj+NLv5VF/AhHsqPIUUwya5oV4CHMUw==",
-        "dependencies": {
-          "System.Runtime.CompilerServices.Unsafe": "6.0.0"
-        }
+        "resolved": "8.0.0",
+        "contentHash": "c9xLpVz6PL9lp/djOWtk5KPDZq3cSYpmXoJQY524EOtuFl5z9ZtsotpsyrDW40U1DRnQSYvcPKEUV0X//u6gkQ=="
       },
       "System.IO.Abstractions": {
         "type": "Transitive",

src/Api/packages.lock.json

@@ -244,11 +244,8 @@
       },
       "System.Diagnostics.DiagnosticSource": {
         "type": "Transitive",
-        "resolved": "6.0.0",
-        "contentHash": "frQDfv0rl209cKm1lnwTgFPzNigy2EKk1BS3uAvHvlBVKe5cymGyHO+Sj+NLv5VF/AhHsqPIUUwya5oV4CHMUw==",
-        "dependencies": {
-          "System.Runtime.CompilerServices.Unsafe": "6.0.0"
-        }
+        "resolved": "8.0.0",
+        "contentHash": "c9xLpVz6PL9lp/djOWtk5KPDZq3cSYpmXoJQY524EOtuFl5z9ZtsotpsyrDW40U1DRnQSYvcPKEUV0X//u6gkQ=="
       },
       "System.IO.Abstractions": {
         "type": "Transitive",

src/Client/packages.lock.json

@@ -325,11 +325,8 @@
       },
       "System.Diagnostics.DiagnosticSource": {
         "type": "Transitive",
-        "resolved": "6.0.0",
-        "contentHash": "frQDfv0rl209cKm1lnwTgFPzNigy2EKk1BS3uAvHvlBVKe5cymGyHO+Sj+NLv5VF/AhHsqPIUUwya5oV4CHMUw==",
-        "dependencies": {
-          "System.Runtime.CompilerServices.Unsafe": "6.0.0"
-        }
+        "resolved": "8.0.0",
+        "contentHash": "c9xLpVz6PL9lp/djOWtk5KPDZq3cSYpmXoJQY524EOtuFl5z9ZtsotpsyrDW40U1DRnQSYvcPKEUV0X//u6gkQ=="
       },
       "System.Diagnostics.EventLog": {
         "type": "Transitive",

src/Configuration/Test/packages.lock.json

@@ -250,11 +250,8 @@
       },
       "System.Diagnostics.DiagnosticSource": {
         "type": "Transitive",
-        "resolved": "6.0.0",
-        "contentHash": "frQDfv0rl209cKm1lnwTgFPzNigy2EKk1BS3uAvHvlBVKe5cymGyHO+Sj+NLv5VF/AhHsqPIUUwya5oV4CHMUw==",
-        "dependencies": {
-          "System.Runtime.CompilerServices.Unsafe": "6.0.0"
-        }
+        "resolved": "8.0.0",
+        "contentHash": "c9xLpVz6PL9lp/djOWtk5KPDZq3cSYpmXoJQY524EOtuFl5z9ZtsotpsyrDW40U1DRnQSYvcPKEUV0X//u6gkQ=="
       },
       "System.IO.Abstractions": {
         "type": "Transitive",

src/Configuration/packages.lock.json

@@ -90,4 +90,4 @@ public override string ToString()
             return $"Identity: {Identity}";
         }
     }
-}
+}

src/Database/Api/DatabaseRegistrationBase.cs

@@ -250,11 +250,8 @@
       },
       "System.Diagnostics.DiagnosticSource": {
         "type": "Transitive",
-        "resolved": "6.0.0",
-        "contentHash": "frQDfv0rl209cKm1lnwTgFPzNigy2EKk1BS3uAvHvlBVKe5cymGyHO+Sj+NLv5VF/AhHsqPIUUwya5oV4CHMUw==",
-        "dependencies": {
-          "System.Runtime.CompilerServices.Unsafe": "6.0.0"
-        }
+        "resolved": "8.0.0",
+        "contentHash": "c9xLpVz6PL9lp/djOWtk5KPDZq3cSYpmXoJQY524EOtuFl5z9ZtsotpsyrDW40U1DRnQSYvcPKEUV0X//u6gkQ=="
       },
       "System.IO.Abstractions": {
         "type": "Transitive",

src/Database/Api/StorageMetadataWrapper.cs

@@ -411,11 +411,8 @@
       },
       "System.Diagnostics.DiagnosticSource": {
         "type": "Transitive",
-        "resolved": "6.0.0",
-        "contentHash": "frQDfv0rl209cKm1lnwTgFPzNigy2EKk1BS3uAvHvlBVKe5cymGyHO+Sj+NLv5VF/AhHsqPIUUwya5oV4CHMUw==",
-        "dependencies": {
-          "System.Runtime.CompilerServices.Unsafe": "6.0.0"
-        }
+        "resolved": "8.0.0",
+        "contentHash": "c9xLpVz6PL9lp/djOWtk5KPDZq3cSYpmXoJQY524EOtuFl5z9ZtsotpsyrDW40U1DRnQSYvcPKEUV0X//u6gkQ=="
       },
       "System.Diagnostics.EventLog": {
         "type": "Transitive",

src/Database/Api/packages.lock.json

@@ -324,11 +324,8 @@
       },
       "System.Diagnostics.DiagnosticSource": {
         "type": "Transitive",
-        "resolved": "6.0.0",
-        "contentHash": "frQDfv0rl209cKm1lnwTgFPzNigy2EKk1BS3uAvHvlBVKe5cymGyHO+Sj+NLv5VF/AhHsqPIUUwya5oV4CHMUw==",
-        "dependencies": {
-          "System.Runtime.CompilerServices.Unsafe": "6.0.0"
-        }
+        "resolved": "8.0.0",
+        "contentHash": "c9xLpVz6PL9lp/djOWtk5KPDZq3cSYpmXoJQY524EOtuFl5z9ZtsotpsyrDW40U1DRnQSYvcPKEUV0X//u6gkQ=="
       },
       "System.IO.Abstractions": {
         "type": "Transitive",

src/Database/DatabaseManager.cs

@@ -36,7 +36,6 @@
 using Monai.Deploy.InformaticsGateway.Services.DicomWeb;
 using Monai.Deploy.InformaticsGateway.Services.Export;
 using Monai.Deploy.InformaticsGateway.Services.Fhir;
-using Monai.Deploy.InformaticsGateway.Services.HealthLevel7;
 using Monai.Deploy.InformaticsGateway.Services.Http;
 using Monai.Deploy.InformaticsGateway.Services.Scp;
 using Monai.Deploy.InformaticsGateway.Services.Scu;

src/Database/MongoDB/Integration.Test/packages.lock.json

@@ -588,4 +588,4 @@ public void Dispose()
 
         #endregion Data Retrieval
     }
-}
+}

src/Database/MongoDB/Repositories/StorageMetadataWrapperRepository.cs

@@ -249,4 +249,4 @@ public void Dispose()
             Status = ServiceStatus.Stopped;
         }
     }
-}
+}

src/Database/MongoDB/packages.lock.json

@@ -241,4 +241,4 @@ public void Dispose()
             GC.SuppressFinalize(this);
         }
     }
-}
+}

src/InformaticsGateway/Logging/Log.8000.HttpServices.cs

@@ -95,4 +95,4 @@ private static string SetIdIfMIssing(string correlationId, JsonNode jsonDoc)
             return jsonDoc[Resources.PropertyId]?.GetValue<string>() ?? string.Empty;
         }
     }
-}
+}

src/InformaticsGateway/Program.cs

@@ -117,4 +117,4 @@ private static string SetIdIfMIssing(string correlationId, XmlNamespaceManager x
             return idNode.Attributes[Resources.AttributeValue]!.Value;
         }
     }
-}
+}

src/InformaticsGateway/Repositories/MonaiServiceLocator.cs

@@ -265,4 +265,4 @@ public void Dispose()
             GC.SuppressFinalize(this);
         }
     }
-}
+}

src/InformaticsGateway/Services/Common/IInputDataPluginEngineFactory.cs

@@ -25,9 +25,10 @@
 using Microsoft.Extensions.Options;
 using Monai.Deploy.InformaticsGateway.Api.Mllp;
 using Monai.Deploy.InformaticsGateway.Configuration;
+using Monai.Deploy.InformaticsGateway.Database.Api.Repositories;
 using Monai.Deploy.InformaticsGateway.Logging;
 
-namespace Monai.Deploy.InformaticsGateway.Services.HealthLevel7
+namespace Monai.Deploy.InformaticsGateway.Api.Mllp
 {
     internal class MllpService : IMllpService
     {
@@ -122,4 +123,4 @@ private async Task EnsureAck(NetworkStream networkStream)
             throw new Hl7SendException("ACK message contains no ACK!");
         }
     }
-}
+}

src/InformaticsGateway/Services/Common/InputDataPluginEngine.cs

@@ -229,4 +229,4 @@ public void Dispose()
             GC.SuppressFinalize(this);
         }
     }
-}
+}

src/InformaticsGateway/Services/Common/OutputDataPluginEngine.cs

@@ -1,4 +1,4 @@
-<!--
+<!--
   ~ Copyright 2021-2023 MONAI Consortium
   ~
   ~ Licensed under the Apache License, Version 2.0 (the "License");

src/InformaticsGateway/Services/Connectors/DataRetrievalService.cs

@@ -134,7 +134,7 @@ public async Task GivenAPayloadThatHasIncompleteUploads_WhenProcessedByTimedEven
 
             file1.SetFailed();
             file2.SetUploaded();
-            await Task.Delay(1001);
+            await Task.Delay(1101);
             payloadAssembler.Dispose();
 
             _repository.Verify(p => p.UpdateAsync(It.Is<Payload>(p => p.State == Payload.PayloadState.Move), It.IsAny<CancellationToken>()), Times.Never());

src/InformaticsGateway/Services/Connectors/PayloadAssembler.cs

@@ -178,4 +178,4 @@ public void GivenAPayload_WhenDequedFromPayloadAssembler_ExpectThePayloadBeProce
             _logger.VerifyLogging($"Payload {payload.PayloadId} added to {service.ServiceName} for processing.", LogLevel.Information, Times.AtLeastOnce());
         }
     }
-}
+}

src/InformaticsGateway/Services/Connectors/PayloadNotificationActionHandler.cs

@@ -411,4 +411,4 @@ public async Task GivenATcpClientWithHl7Messages_ShouldntAdddBlankPlugin()
             _hl7DataPlugInEngine.Verify(p => p.Configure(It.IsAny<IReadOnlyList<string>>()), Times.Never());
         }
     }
-}
+}