change to how dicomTag are stored

Signed-off-by: Neil South <[email protected]>
Project-MONAI · Aug 9, 2023 · af896bc · af896bc
1 parent 6efcc20
commit af896bc
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Showing 15 changed files with 134 additions and 17 deletions.
diff --git a/src/Api/Storage/RemoteAppExecution.cs b/src/Api/Storage/RemoteAppExecution.cs
@@ -16,22 +16,24 @@
 
 using System;
 using System.Collections.Generic;
-using FellowOakDicom;
+using System.Text.Json.Serialization;
 using Monai.Deploy.Messaging.Events;
 
 namespace Monai.Deploy.InformaticsGateway.Api.Storage
 {
     public class RemoteAppExecution
     {
+        [JsonPropertyName("_id")]
+        public string Id { get; set; } = default!;
         public DateTime RequestTime { get; set; } = DateTime.UtcNow;
         public string ExportTaskId { get; set; } = string.Empty;
         public string WorkflowInstanceId { get; set; } = string.Empty;
         public string CorrelationId { get; set; } = string.Empty;
         public string? StudyUid { get; set; }
-        public string? OutgoingUid { get; set; }
+        public string? OutgoingUid { get { return Id; } set { Id = value ?? ""; } }
         public List<DestinationApplicationEntity> ExportDetails { get; set; } = new();
         public List<string> Files { get; set; } = new();
         public FileExportStatus Status { get; set; }
-        public Dictionary<DicomTag, string> OriginalValues { get; set; } = new();
+        public Dictionary<string, string> OriginalValues { get; set; } = new();
     }
 }
diff --git a/src/Database/MongoDB/Configurations/MongoDBOptions.cs b/src/Database/MongoDB/Configurations/MongoDBOptions.cs
@@ -21,6 +21,6 @@ namespace Monai.Deploy.InformaticsGateway.Database.MongoDB.Configurations
     public class MongoDBOptions
     {
         [ConfigurationKeyName("DatabaseName")]
-        public string DaatabaseName { get; set; } = string.Empty;
+        public string DatabaseName { get; set; } = string.Empty;
     }
 }
diff --git a/src/Database/MongoDB/Integration.Test/MongoDatabaseFixture.cs b/src/Database/MongoDB/Integration.Test/MongoDatabaseFixture.cs
@@ -40,8 +40,8 @@ public class MongoDatabaseFixture
         public MongoDatabaseFixture()
         {
             Client = new MongoClient("mongodb://root:rootpassword@localhost:27017");
-            Options = Microsoft.Extensions.Options.Options.Create(new MongoDBOptions { DaatabaseName = $"IGTest" });
-            Database = Client.GetDatabase(Options.Value.DaatabaseName);
+            Options = Microsoft.Extensions.Options.Options.Create(new MongoDBOptions { DatabaseName = $"IGTest" });
+            Database = Client.GetDatabase(Options.Value.DatabaseName);
 
             var migration = new MongoDatabaseMigrationManager();
             migration.Migrate(null!);

diff --git a/src/Database/MongoDB/Integration.Test/RemoteAppRepositoryTest.cs b/src/Database/MongoDB/Integration.Test/RemoteAppRepositoryTest.cs
@@ -0,0 +1,106 @@
+/*
+ * 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 FellowOakDicom;
+using Microsoft.EntityFrameworkCore;
+using Microsoft.Extensions.DependencyInjection;
+using Microsoft.Extensions.Logging;
+using Microsoft.Extensions.Options;
+using Microsoft.VisualBasic;
+using Monai.Deploy.InformaticsGateway.Api.Storage;
+using Monai.Deploy.InformaticsGateway.Configuration;
+using Monai.Deploy.InformaticsGateway.Database.EntityFramework.Test;
+using Monai.Deploy.InformaticsGateway.Database.MongoDB.Repositories;
+using MongoDB.Driver;
+using Moq;
+namespace Monai.Deploy.InformaticsGateway.Database.MongoDB.Integration.Test
+{
+    [Collection("MongoDatabase")]
+    public class RemoteAppRepositoryTest
+    {
+        private readonly MongoDatabaseFixture _databaseFixture;
+
+        private readonly Mock<IServiceScopeFactory> _serviceScopeFactory;
+        private readonly Mock<ILogger<RemoteAppExecutionRepository>> _logger;
+        private readonly IOptions<InformaticsGatewayConfiguration> _options;
+
+        private readonly Mock<IServiceScope> _serviceScope;
+        private readonly IServiceProvider _serviceProvider;
+
+        public RemoteAppRepositoryTest(MongoDatabaseFixture databaseFixture)
+        {
+            _databaseFixture = databaseFixture ?? throw new ArgumentNullException(nameof(databaseFixture));
+
+            _serviceScopeFactory = new Mock<IServiceScopeFactory>();
+            _logger = new Mock<ILogger<RemoteAppExecutionRepository>>();
+            _options = Options.Create(new InformaticsGatewayConfiguration());
+
+            _serviceScope = new Mock<IServiceScope>();
+            var services = new ServiceCollection();
+            services.AddScoped(p => _logger.Object);
+            services.AddScoped(p => databaseFixture.Client);
+
+            _serviceProvider = services.BuildServiceProvider();
+            _serviceScopeFactory.Setup(p => p.CreateScope()).Returns(_serviceScope.Object);
+            _serviceScope.Setup(p => p.ServiceProvider).Returns(_serviceProvider);
+
+            _options.Value.Database.Retries.DelaysMilliseconds = new[] { 1, 1, 1 };
+            _logger.Setup(p => p.IsEnabled(It.IsAny<LogLevel>())).Returns(true);
+        }
+
+        [Fact]
+        public async Task GivenAexecution_WhenAddingToDatabase_ExpectItToBeSaved()
+        {
+            var outgoingUid = Guid.NewGuid().ToString();
+            var dataset = new DicomDataset();
+            var date = new DateTime(2023, 5, 21, 6, 7, 8).ToUniversalTime();
+
+            var execution = new RemoteAppExecution
+            {
+                CorrelationId = Guid.NewGuid().ToString(),
+                ExportTaskId = "ExportTaskId",
+                WorkflowInstanceId = "WorkflowInstanceId",
+                OutgoingUid = outgoingUid,
+                StudyUid = Guid.NewGuid().ToString(),
+                RequestTime = date,
+                OriginalValues = new Dictionary<string, string> {
+                    { DicomTag.StudyInstanceUID.ToString(), "StudyInstanceUID" },
+                    { DicomTag.SeriesInstanceUID.ToString(), "SeriesInstanceUID" }
+                }
+            };
+
+
+            var store = new RemoteAppExecutionRepository(_serviceScopeFactory.Object, _logger.Object, _options, _databaseFixture.Options);
+            await store.AddAsync(execution).ConfigureAwait(false);
+
+            var collection = _databaseFixture.Database.GetCollection<RemoteAppExecution>(nameof(RemoteAppExecution));
+            var actual = await collection.Find(p => p.OutgoingUid == execution.OutgoingUid).FirstOrDefaultAsync().ConfigureAwait(false);
+
+            Task.Delay(1000).Wait();
+            Assert.NotNull(actual);
+            Assert.Equal(execution.CorrelationId, actual!.CorrelationId);
+            Assert.Equal(execution.ExportTaskId, actual!.ExportTaskId);
+            Assert.Equal(execution.WorkflowInstanceId, actual!.WorkflowInstanceId);
+            Assert.Equal(execution.OutgoingUid, actual!.OutgoingUid);
+            Assert.Equal(execution.CorrelationId, actual!.CorrelationId);
+            Assert.Equal(execution.WorkflowInstanceId, actual!.WorkflowInstanceId);
+            Assert.Equal(execution.StudyUid, actual!.StudyUid);
+            Assert.Equal(execution.RequestTime, actual!.RequestTime);
+            Assert.Equal(execution.OriginalValues, actual!.OriginalValues);
+            Assert.Equal(2, actual!.OriginalValues.Count);
+        }
+    }
+}
diff --git a/src/Database/MongoDB/Repositories/DestinationApplicationEntityRepository.cs b/src/Database/MongoDB/Repositories/DestinationApplicationEntityRepository.cs
@@ -57,7 +57,7 @@ public DestinationApplicationEntityRepository(
                 (exception, timespan, count, context) => _logger.DatabaseErrorRetry(timespan, count, exception));
 
             var mongoDbClient = _scope.ServiceProvider.GetRequiredService<IMongoClient>();
-            var mongoDatabase = mongoDbClient.GetDatabase(mongoDbOptions.Value.DaatabaseName);
+            var mongoDatabase = mongoDbClient.GetDatabase(mongoDbOptions.Value.DatabaseName);
             _collection = mongoDatabase.GetCollection<DestinationApplicationEntity>(nameof(DestinationApplicationEntity));
             CreateIndexes();
         }

diff --git a/src/Database/MongoDB/Repositories/DicomAssociationInfoRepository.cs b/src/Database/MongoDB/Repositories/DicomAssociationInfoRepository.cs
@@ -55,7 +55,7 @@ public DicomAssociationInfoRepository(
                 (exception, timespan, count, context) => _logger.DatabaseErrorRetry(timespan, count, exception));
 
             var mongoDbClient = _scope.ServiceProvider.GetRequiredService<IMongoClient>();
-            var mongoDatabase = mongoDbClient.GetDatabase(mongoDbOptions.Value.DaatabaseName);
+            var mongoDatabase = mongoDbClient.GetDatabase(mongoDbOptions.Value.DatabaseName);
             _collection = mongoDatabase.GetCollection<DicomAssociationInfo>(nameof(DicomAssociationInfo));
         }
 

diff --git a/src/Database/MongoDB/Repositories/InferenceRequestRepository.cs b/src/Database/MongoDB/Repositories/InferenceRequestRepository.cs
@@ -59,7 +59,7 @@ public InferenceRequestRepository(
                 (exception, timespan, count, context) => _logger.DatabaseErrorRetry(timespan, count, exception));
 
             var mongoDbClient = _scope.ServiceProvider.GetRequiredService<IMongoClient>();
-            var mongoDatabase = mongoDbClient.GetDatabase(mongoDbOptions.Value.DaatabaseName);
+            var mongoDatabase = mongoDbClient.GetDatabase(mongoDbOptions.Value.DatabaseName);
             _collection = mongoDatabase.GetCollection<InferenceRequest>(nameof(InferenceRequest));
             CreateIndexes();
         }

diff --git a/src/Database/MongoDB/Repositories/MonaiApplicationEntityRepository.cs b/src/Database/MongoDB/Repositories/MonaiApplicationEntityRepository.cs
@@ -57,7 +57,7 @@ public MonaiApplicationEntityRepository(
                 (exception, timespan, count, context) => _logger.DatabaseErrorRetry(timespan, count, exception));
 
             var mongoDbClient = _scope.ServiceProvider.GetRequiredService<IMongoClient>();
-            var mongoDatabase = mongoDbClient.GetDatabase(mongoDbOptions.Value.DaatabaseName);
+            var mongoDatabase = mongoDbClient.GetDatabase(mongoDbOptions.Value.DatabaseName);
             _collection = mongoDatabase.GetCollection<MonaiApplicationEntity>(nameof(MonaiApplicationEntity));
             CreateIndexes();
         }

diff --git a/src/Database/MongoDB/Repositories/PayloadRepository.cs b/src/Database/MongoDB/Repositories/PayloadRepository.cs
@@ -57,7 +57,7 @@ public PayloadRepository(
                 (exception, timespan, count, context) => _logger.DatabaseErrorRetry(timespan, count, exception));
 
             var mongoDbClient = _scope.ServiceProvider.GetRequiredService<IMongoClient>();
-            var mongoDatabase = mongoDbClient.GetDatabase(mongoDbOptions.Value.DaatabaseName);
+            var mongoDatabase = mongoDbClient.GetDatabase(mongoDbOptions.Value.DatabaseName);
             _collection = mongoDatabase.GetCollection<Payload>(nameof(Payload));
             CreateIndexes();
         }

diff --git a/src/Database/MongoDB/Repositories/RemoteAppExecutionRepository.cs b/src/Database/MongoDB/Repositories/RemoteAppExecutionRepository.cs
@@ -54,7 +54,7 @@ public RemoteAppExecutionRepository(IServiceScopeFactory serviceScopeFactory,
                 (exception, timespan, count, context) => _logger.DatabaseErrorRetry(timespan, count, exception));
 
             var mongoDbClient = _scope.ServiceProvider.GetRequiredService<IMongoClient>();
-            var mongoDatabase = mongoDbClient.GetDatabase(mongoDbOptions.Value.DaatabaseName);
+            var mongoDatabase = mongoDbClient.GetDatabase(mongoDbOptions.Value.DatabaseName);
             _collection = mongoDatabase.GetCollection<RemoteAppExecution>(nameof(RemoteAppExecution));
             CreateIndexes();
         }

diff --git a/src/Database/MongoDB/Repositories/SourceApplicationEntityRepository.cs b/src/Database/MongoDB/Repositories/SourceApplicationEntityRepository.cs
@@ -57,7 +57,7 @@ public SourceApplicationEntityRepository(
                 (exception, timespan, count, context) => _logger.DatabaseErrorRetry(timespan, count, exception));
 
             var mongoDbClient = _scope.ServiceProvider.GetRequiredService<IMongoClient>();
-            var mongoDatabase = mongoDbClient.GetDatabase(mongoDbOptions.Value.DaatabaseName);
+            var mongoDatabase = mongoDbClient.GetDatabase(mongoDbOptions.Value.DatabaseName);
             _collection = mongoDatabase.GetCollection<SourceApplicationEntity>(nameof(SourceApplicationEntity));
             CreateIndexes();
         }

diff --git a/src/Database/MongoDB/Repositories/StorageMetadataWrapperRepository.cs b/src/Database/MongoDB/Repositories/StorageMetadataWrapperRepository.cs
@@ -59,7 +59,7 @@ public StorageMetadataWrapperRepository(
                 (exception, timespan, count, context) => _logger.DatabaseErrorRetry(timespan, count, exception));
 
             var mongoDbClient = _scope.ServiceProvider.GetRequiredService<IMongoClient>();
-            var mongoDatabase = mongoDbClient.GetDatabase(mongoDbOptions.Value.DaatabaseName);
+            var mongoDatabase = mongoDbClient.GetDatabase(mongoDbOptions.Value.DatabaseName);
             _collection = mongoDatabase.GetCollection<StorageMetadataWrapper>(nameof(StorageMetadataWrapper));
             CreateIndexes();
         }

diff --git a/src/InformaticsGateway/ExecutionPlugins/ExternalAppIncoming.cs b/src/InformaticsGateway/ExecutionPlugins/ExternalAppIncoming.cs
@@ -62,7 +62,8 @@ public ExternalAppIncoming(
             }
             foreach (var key in remoteAppExecution.OriginalValues.Keys)
             {
-                dicomFile.Dataset.AddOrUpdate(key, remoteAppExecution.OriginalValues[key]);
+                var (group, element) = Parse(key);
+                dicomFile.Dataset.AddOrUpdate(new DicomTag(group, element), remoteAppExecution.OriginalValues[key]);
             }
 
             fileMetadata.WorkflowInstanceId = remoteAppExecution.WorkflowInstanceId;
@@ -71,6 +72,13 @@ public ExternalAppIncoming(
             return (dicomFile, fileMetadata);
         }
 
+        private (ushort group, ushort element) Parse(string input)
+        {
+            var trim = input.Substring(1, input.Length - 2);
+            var array = trim.Split(',', StringSplitOptions.TrimEntries | StringSplitOptions.RemoveEmptyEntries);
+            return (Convert.ToUInt16(array[0], 16), Convert.ToUInt16(array[1], 16));
+        }
+
         private static DicomTag[] GetTags(string values)
         {
             var names = values.Split(',', StringSplitOptions.RemoveEmptyEntries | StringSplitOptions.TrimEntries);

diff --git a/src/InformaticsGateway/ExecutionPlugins/ExternalAppOutgoing.cs b/src/InformaticsGateway/ExecutionPlugins/ExternalAppOutgoing.cs
@@ -15,6 +15,7 @@
  */
 
 using System;
+using System.Data;
 using System.Linq;
 using System.Threading;
 using System.Threading.Tasks;
@@ -61,7 +62,7 @@ public ExternalAppOutgoing(
             {
                 if (dicomFile.Dataset.TryGetString(tag, out var value))
                 {
-                    remoteAppExecution.OriginalValues.Add(tag, value);
+                    remoteAppExecution.OriginalValues.Add(tag.ToString(), value);
                     SetTag(dicomFile, tag);
                 }
             }

diff --git a/src/InformaticsGateway/Test/Services/Common/ExternalAppPluginTest.cs b/src/InformaticsGateway/Test/Services/Common/ExternalAppPluginTest.cs
@@ -211,7 +211,7 @@ public async Task ExternalAppPlugin_Should_Repare_StudyUid()
             {
                 OutgoingUid = outboundStudyUid,
                 StudyUid = originalStudyUid,
-                OriginalValues = { { DicomTag.StudyInstanceUID, originalStudyUid } }
+                OriginalValues = { { DicomTag.StudyInstanceUID.ToString(), originalStudyUid } }
             };
 
             _repository.Setup(r => r.GetAsync(It.IsAny<string>(), It.IsAny<CancellationToken>()))