Merge pull request #494 from Project-MONAI/AI-300

Ai 300

Author: neildsouth

doc/dependency_decisions.yml

@@ -774,16 +774,16 @@
   - :who: neilsouth
     :why: Apache-2.0 (https://github.com/Project-MONAI/monai-deploy-messaging/raw/main/LICENSE)
     :versions:
-    - 1.0.3
-    - 1.0.4
+    - 1.0.5-rc0006
+    - 1.0.5
     :when: 2023-10-13 18:06:21.511789690 Z
 - - :approve
   - Monai.Deploy.Messaging.RabbitMQ
   - :who: neilsouth
     :why: Apache-2.0 (https://github.com/Project-MONAI/monai-deploy-messaging/raw/main/LICENSE)
     :versions:
-    - 1.0.3
-    - 1.0.4
+    - 1.0.5-rc0006
+    - 1.0.5
     :when: 2023-10-13 18:06:21.511789690 Z
 - - :approve
   - Monai.Deploy.Storage

src/Api/Hl7ApplicationConfigEntity.cs

@@ -20,6 +20,7 @@
 using System.ComponentModel.DataAnnotations;
 using System.Linq;
 using FellowOakDicom;
+using Monai.Deploy.InformaticsGateway.Api.Storage;
 using Monai.Deploy.InformaticsGateway.Common;
 using Newtonsoft.Json;
 

src/Api/BaseApplicationEntity.cs renamed to src/Api/Models/BaseApplicationEntity.cs

@@ -17,8 +17,9 @@
 
 using System;
 using System.Security.Claims;
+using Monai.Deploy.InformaticsGateway.Api.Storage;
 
-namespace Monai.Deploy.InformaticsGateway.Api
+namespace Monai.Deploy.InformaticsGateway.Api.Models
 {
     /// <summary>
     /// DICOM Application Entity or AE.

src/Api/DestinationApplicationEntity.cs renamed to src/Api/Models/DestinationApplicationEntity.cs

@@ -15,7 +15,7 @@
  * limitations under the License.
  */
 
-namespace Monai.Deploy.InformaticsGateway.Api
+namespace Monai.Deploy.InformaticsGateway.Api.Models
 {
     /// <summary>
     /// Destination Application Entity

src/Api/DicomAssociationInfo.cs renamed to src/Api/Models/DicomAssociationInfo.cs

@@ -16,8 +16,9 @@
 
 using System;
 using System.Collections.Generic;
+using Monai.Deploy.InformaticsGateway.Api.Storage;
 
-namespace Monai.Deploy.InformaticsGateway.Api
+namespace Monai.Deploy.InformaticsGateway.Api.Models
 {
     public class DicomAssociationInfo : MongoDBEntityBase
     {

src/Api/ExportRequestDataMessage.cs renamed to src/Api/Models/ExportRequestDataMessage.cs

@@ -20,7 +20,7 @@
 using Monai.Deploy.InformaticsGateway.Api.PlugIns;
 using Monai.Deploy.Messaging.Events;
 
-namespace Monai.Deploy.InformaticsGateway.Api
+namespace Monai.Deploy.InformaticsGateway.Api.Models
 {
     public class ExportRequestDataMessage
     {

src/Api/Models/ExternalAppDetails.cs

@@ -0,0 +1,39 @@
+/*
+ * 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 Monai.Deploy.InformaticsGateway.Api.Storage;
+
+namespace Monai.Deploy.InformaticsGateway.Api.Models
+{
+    public class ExternalAppDetails : MongoDBEntityBase
+    {
+        public string StudyInstanceUid { get; set; } = string.Empty;
+
+        public string StudyInstanceUidOutBound { get; set; } = string.Empty;
+
+        public string WorkflowInstanceId { get; set; } = string.Empty;
+
+        public string ExportTaskID { get; set; } = string.Empty;
+
+        public string CorrelationId { get; set; } = string.Empty;
+
+        public string? DestinationFolder { get; set; }
+
+        public string PatientId { get; set; } = string.Empty;
+
+        public string PatientIdOutBound { get; set; } = string.Empty;
+    }
+}

src/Api/MonaiApplicationEntity.cs renamed to src/Api/Models/MonaiApplicationEntity.cs

@@ -21,8 +21,9 @@
 using System.ComponentModel.DataAnnotations.Schema;
 using System.Security.Claims;
 using Monai.Deploy.InformaticsGateway.Api.PlugIns;
+using Monai.Deploy.InformaticsGateway.Api.Storage;
 
-namespace Monai.Deploy.InformaticsGateway.Api
+namespace Monai.Deploy.InformaticsGateway.Api.Models
 {
     /// <summary>
     /// MONAI Application Entity

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

@@ -55,8 +55,8 @@
     <PackageReference Include="fo-dicom" Version="5.1.1" />
     <PackageReference Include="Macross.Json.Extensions" Version="3.0.0" />
     <PackageReference Include="Microsoft.EntityFrameworkCore.Abstractions" Version="6.0.22" />
-    <PackageReference Include="Monai.Deploy.Messaging" Version="1.0.4" />
-    <PackageReference Include="Monai.Deploy.Messaging.RabbitMQ" Version="1.0.4" />
+    <PackageReference Include="Monai.Deploy.Messaging" Version="1.0.5-rc0006" />
+    <PackageReference Include="Monai.Deploy.Messaging.RabbitMQ" Version="1.0.5-rc0006" />
     <PackageReference Include="Monai.Deploy.Storage" Version="0.2.18" />
   </ItemGroup>
 

src/Api/PlugIns/IOutputDataPlugin.cs

@@ -16,6 +16,7 @@
 
 using System.Threading.Tasks;
 using FellowOakDicom;
+using Monai.Deploy.InformaticsGateway.Api.Models;
 
 namespace Monai.Deploy.InformaticsGateway.Api.PlugIns
 {

src/Api/PlugIns/IOutputDataPluginEngine.cs

@@ -16,6 +16,7 @@
 
 using System.Collections.Generic;
 using System.Threading.Tasks;
+using Monai.Deploy.InformaticsGateway.Api.Models;
 
 namespace Monai.Deploy.InformaticsGateway.Api.PlugIns
 {

src/Api/SourceApplicationEntity.cs

@@ -15,6 +15,8 @@
  * limitations under the License.
  */
 
+using Monai.Deploy.InformaticsGateway.Api.Models;
+
 namespace Monai.Deploy.InformaticsGateway.Api
 {
     /// <summary>

src/Api/Storage/DicomFileStorageMetadata.cs

@@ -36,7 +36,7 @@ public sealed record DicomFileStorageMetadata : FileStorageMetadata
         /// Gets or set the Study Instance UID of the DICOM instance.
         /// </summary>
         [JsonPropertyName("studyInstanceUid")]
-        public string StudyInstanceUid { get; init; } = default!;
+        public string StudyInstanceUid { get; set; } = default!;
 
         /// <summary>
         /// Gets or set the Series Instance UID of the DICOM instance.
@@ -93,6 +93,15 @@ public DicomFileStorageMetadata(string associationId, string identifier, string
             StudyInstanceUid = studyInstanceUid;
             SeriesInstanceUid = seriesInstanceUid;
             SopInstanceUid = sopInstanceUid;
+            SetupFilePaths(associationId);
+
+            DataOrigin.DataService = dataService;
+            DataOrigin.Source = callingAeTitle;
+            DataOrigin.Destination = calledAeTitle;
+        }
+
+        private void SetupFilePaths(string associationId)
+        {
             File = new StorageObjectMetadata(FileExtension)
             {
                 TemporaryPath = string.Join(PathSeparator, associationId, DataTypeDirectoryName, $"{Guid.NewGuid()}{FileExtension}"),
@@ -106,16 +115,45 @@ public DicomFileStorageMetadata(string associationId, string identifier, string
                 UploadPath = $"{File.UploadPath}{DicomJsonFileExtension}",
                 ContentType = DicomJsonContentType,
             };
+        }
 
-            DataOrigin.DataService = dataService;
-            DataOrigin.Source = callingAeTitle;
-            DataOrigin.Destination = calledAeTitle;
+        public void SetupGivenFilePaths(string? DestinationFolder)
+        {
+            if (DestinationFolder is null)
+            {
+                return;
+            }
+
+            if (DestinationFolder.EndsWith('/'))
+            {
+                DestinationFolder = DestinationFolder.Remove(DestinationFolder.Length - 1);
+            }
+
+            File = new StorageObjectMetadata(FileExtension)
+            {
+                TemporaryPath = string.Join(PathSeparator, DestinationFolder, $"Temp{PathSeparator}{Guid.NewGuid()}{FileExtension}"),
+                UploadPath = string.Join(PathSeparator, DestinationFolder, $"{SopInstanceUid}{FileExtension}"),
+                ContentType = DicomContentType,
+                DestinationFolderOverride = true,
+            };
+
+            JsonFile = new StorageObjectMetadata(DicomJsonFileExtension)
+            {
+                TemporaryPath = $"{File.TemporaryPath}{DicomJsonFileExtension}",
+                UploadPath = $"{File.UploadPath}{DicomJsonFileExtension}",
+                ContentType = DicomJsonContentType,
+                DestinationFolderOverride = true,
+            };
+
+            //DestinationFolderNeil = DestinationFolder;
         }
 
+        public void SetStudyInstanceUid(string newStudyInstanceUid) => StudyInstanceUid = newStudyInstanceUid;
+
         public override void SetFailed()
         {
             base.SetFailed();
             JsonFile.SetFailed();
         }
     }
-}
+}

src/Api/Storage/FileStorageMetadata.cs

@@ -104,6 +104,9 @@ public abstract record FileStorageMetadata
         [JsonPropertyName("payloadId")]
         public string? PayloadId { get; set; }
 
+       // [JsonPropertyName("destinationFolder")]
+       //public string? DestinationFolderNeil { get; set; }
+
         /// <summary>
         /// DO NOT USE
         /// This constructor is intended for JSON serializer.
@@ -162,4 +165,4 @@ public static string IpAddress()
             return "127.0.0.1";
         }
     }
-}
+}

src/Api/MongoDBEntityBase.cs renamed to src/Api/Storage/MongoDBEntityBase.cs

@@ -16,7 +16,7 @@
 
 using System;
 
-namespace Monai.Deploy.InformaticsGateway.Api
+namespace Monai.Deploy.InformaticsGateway.Api.Storage
 {
     public abstract class MongoDBEntityBase
     {

src/Api/Storage/Payload.cs

@@ -86,6 +86,8 @@ public TimeSpan Elapsed
 
         public int FilesFailedToUpload { get => Files.Count(p => p.IsUploadFailed); }
 
+        public string DestinationFolder { get; set; } = string.Empty;
+
         public Payload(string key, string correlationId, string? workflowInstanceId, string? taskId, DataOrigin dataTrigger, uint timeout)
         {
             Guard.Against.NullOrWhiteSpace(key, nameof(key));
@@ -106,7 +108,7 @@ public Payload(string key, string correlationId, string? workflowInstanceId, str
             DataTrigger = dataTrigger;
         }
 
-        public Payload(string key, string correlationId, string? workflowInstanceId, string? taskId, DataOrigin dataTrigger, uint timeout, string? payloadId = null) :
+        public Payload(string key, string correlationId, string? workflowInstanceId, string? taskId, DataOrigin dataTrigger, uint timeout, string? payloadId = null, string? DestinationFolder = null) :
             this(key, correlationId, workflowInstanceId, taskId, dataTrigger, timeout)
         {
             Guard.Against.NullOrWhiteSpace(key, nameof(key));
@@ -119,6 +121,7 @@ public Payload(string key, string correlationId, string? workflowInstanceId, str
             {
                 PayloadId = Guid.Parse(payloadId);
             }
+            DestinationFolder ??= string.Empty;
         }
 
         public void Add(FileStorageMetadata value)
@@ -132,6 +135,11 @@ public void Add(FileStorageMetadata value)
                 DataOrigins.Add(value.DataOrigin);
             }
 
+            //if (string.IsNullOrWhiteSpace(value.DestinationFolderNeil) is false)
+            //{
+            //    DestinationFolder = value.DestinationFolderNeil;
+            //}
+
             _lastReceived.Reset();
             _lastReceived.Start();
         }

src/Api/Storage/StorageObjectMetadata.cs

@@ -88,6 +88,9 @@ public class StorageObjectMetadata
         [JsonPropertyName("isMoveCompleted"), JsonInclude]
         public bool IsMoveCompleted { get; private set; } = default!;
 
+        [JsonPropertyName("destinationFolderOverride")]
+        public bool DestinationFolderOverride { get; set; } = false;
+
         public StorageObjectMetadata(string fileExtension)
         {
             Guard.Against.NullOrWhiteSpace(fileExtension, nameof(fileExtension));
@@ -111,7 +114,11 @@ public string GetPayloadPath(Guid payloadId)
         {
             Guard.Against.Null(payloadId, nameof(payloadId));
 
-            return $"{payloadId}{FileStorageMetadata.PathSeparator}{UploadPath}";
+            if (DestinationFolderOverride is false)
+            {
+                return $"{payloadId}{FileStorageMetadata.PathSeparator}{UploadPath}";
+            }
+            return $"{UploadPath}";
         }
 
         public void SetUploaded(string bucketName)

src/Api/Test/BaseApplicationEntityTest.cs

@@ -14,6 +14,7 @@
  * limitations under the License.
  */
 
+using Monai.Deploy.InformaticsGateway.Api.Models;
 using Xunit;
 
 namespace Monai.Deploy.InformaticsGateway.Api.Test

src/Api/Test/DestinationApplicationEntityTest.cs

@@ -14,6 +14,7 @@
  * limitations under the License.
  */
 
+using Monai.Deploy.InformaticsGateway.Api.Models;
 using Xunit;
 
 namespace Monai.Deploy.InformaticsGateway.Api.Test

src/Api/Test/MonaiApplicationEntityTest.cs

@@ -14,6 +14,7 @@
  * limitations under the License.
  */
 
+using Monai.Deploy.InformaticsGateway.Api.Models;
 using Xunit;
 
 namespace Monai.Deploy.InformaticsGateway.Api.Test

src/Api/Test/Storage/DicomFileStorageMetadataTest.cs

@@ -89,5 +89,40 @@ public void GivenDicomFileStorageMetadata_WhenGetPayloadPathIsCalled_APayyloadPa
             Assert.Equal($"{payloadId}/{metadata.File.UploadPath}", metadata.File.GetPayloadPath(payloadId));
             Assert.Equal($"{payloadId}/{metadata.JsonFile.UploadPath}", metadata.JsonFile.GetPayloadPath(payloadId));
         }
+
+
+        [Fact]
+        public void StudyInstanceUid_Set_ValidValue()
+        {
+            // Arrange
+            var metadata = new DicomFileStorageMetadata();
+
+            // Act
+            metadata.StudyInstanceUid = "12345";
+
+            // Assert
+            Assert.Equal("12345", metadata.StudyInstanceUid);
+        }
+
+        [Fact]
+        public void SeriesInstanceUid_Set_ValidValue()
+        {
+            // Arrange
+            var metadata = new DicomFileStorageMetadata { SeriesInstanceUid = "67890" };
+
+            // Assert
+            Assert.Equal("67890", metadata.SeriesInstanceUid);
+        }
+
+        [Fact]
+        public void SopInstanceUid_Set_ValidValue()
+        {
+            // Arrange
+            var metadata = new DicomFileStorageMetadata { SopInstanceUid = "ABCDE" };
+
+            // Assert
+            Assert.Equal("ABCDE", metadata.SopInstanceUid);
+        }
+
     }
-}
+}