Add MongoDB support

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

Author: mocsharp

.github/workflows/ci.yml

@@ -235,9 +235,11 @@ jobs:
     strategy:
       matrix:
         feature: [AcrApi, DicomDimseScp, DicomDimseScu, DicomWebExport, DicomWebStow, HealthLevel7, Fhir]
+        database: [ef, mongodb]
       fail-fast: false
     env:
       TAG: ${{ needs.build.outputs.TAG }}
+      DOTNET_TEST: ${{ matrix.database }}
     steps:
       - name: Checkout repository
         uses: actions/checkout@v3

docker-compose/docker-compose.yml

@@ -68,7 +68,7 @@ services:
     networks:
       - monaideploy
     healthcheck:
-      test: echo 'db.runCommand("ping").ok' | mongo localhost:27017/productiondb --quiet
+      test: echo 'db.runCommand("ping").ok' | mongosh localhost:27017/productiondb --quiet
       interval: 10s
       timeout: 10s
       retries: 5

src/Api/BaseApplicationEntity.cs

@@ -23,7 +23,7 @@ namespace Monai.Deploy.InformaticsGateway.Api
     /// <remarks>
     /// * [Application Entity](http://www.otpedia.com/entryDetails.cfm?id=137)
     /// </remarks>
-    public class BaseApplicationEntity
+    public class BaseApplicationEntity : MongoDBEntityBase
     {
         /// <summary>
         /// Gets or sets the unique name used to identify a DICOM application entity.

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

@@ -30,7 +30,7 @@
     </PackageReference>
     <PackageReference Include="Macross.Json.Extensions" Version="3.0.0" />
     <PackageReference Include="Microsoft.EntityFrameworkCore.Abstractions" Version="6.0.10" />
-    <PackageReference Include="Monai.Deploy.Messaging" Version="0.1.11" />
+    <PackageReference Include="Monai.Deploy.Messaging" Version="0.1.17-rc0020" />
     <PackageReference Include="Monai.Deploy.Storage" Version="0.2.10" />
   </ItemGroup>
 

src/Api/MonaiApplicationEntity.cs

@@ -15,6 +15,7 @@
  * limitations under the License.
  */
 
+using System;
 using System.Collections.Generic;
 using System.ComponentModel.DataAnnotations;
 using System.ComponentModel.DataAnnotations.Schema;
@@ -44,7 +45,7 @@ namespace Monai.Deploy.InformaticsGateway.Api
     /// }
     /// </code>
     /// </example>
-    public class MonaiApplicationEntity
+    public class MonaiApplicationEntity : MongoDBEntityBase
     {
         /// <summary>
         /// Gets or sets the name of a MONAI DICOM application entity.
@@ -106,20 +107,11 @@ public void SetDefaultValues()
                 Grouping = "0020,000D";
             }
 
-            if (Workflows is null)
-            {
-                Workflows = new List<string>();
-            }
+            Workflows ??= new List<string>();
 
-            if (IgnoredSopClasses is null)
-            {
-                IgnoredSopClasses = new List<string>();
-            }
+            IgnoredSopClasses ??= new List<string>();
 
-            if (AllowedSopClasses is null)
-            {
-                AllowedSopClasses = new List<string>();
-            }
+            AllowedSopClasses ??= new List<string>();
         }
     }
 }

src/Api/MongoDBEntityBase.cs

@@ -0,0 +1,39 @@
+/*
+ * 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 System;
+
+namespace Monai.Deploy.InformaticsGateway.Api
+{
+    public abstract class MongoDBEntityBase
+    {
+        /// <summary>
+        /// Gets or set the MongoDB associated identifier.
+        /// </summary>
+        public Guid Id { get; set; }
+
+        /// <summary>
+        /// Gets or set the date and time the objects first created.
+        /// </summary>
+        public DateTime DateTimeCreated { get; set; }
+
+        protected MongoDBEntityBase()
+        {
+            Id = Guid.NewGuid();
+            DateTimeCreated = DateTime.UtcNow;
+        }
+    }
+}

src/Api/Storage/Payload.cs

@@ -46,7 +46,7 @@ public enum PayloadState
         private readonly Stopwatch _lastReceived;
         private bool _disposedValue;
 
-        public Guid Id { get; }
+        public Guid PayloadId { get; }
 
         public uint Timeout { get; init; }
 
@@ -66,22 +66,23 @@ public enum PayloadState
 
         public bool HasTimedOut { get => ElapsedTime().TotalSeconds >= Timeout; }
 
-        public TimeSpan Elapsed { get { return DateTime.UtcNow.Subtract(DateTimeCreated); } }
+        public TimeSpan Elapsed
+        { get { return DateTime.UtcNow.Subtract(DateTimeCreated); } }
 
         public string CallingAeTitle { get => Files.OfType<DicomFileStorageMetadata>().Select(p => p.CallingAeTitle).FirstOrDefault(); }
 
         public string CalledAeTitle { get => Files.OfType<DicomFileStorageMetadata>().Select(p => p.CalledAeTitle).FirstOrDefault(); }
 
         public Payload(string key, string correlationId, uint timeout)
         {
-            Guard.Against.NullOrWhiteSpace(key, nameof(key));
+            Guard.Against.NullOrWhiteSpace(key);
 
             Files = new List<FileStorageMetadata>();
             _lastReceived = new Stopwatch();
 
             CorrelationId = correlationId;
             DateTimeCreated = DateTime.UtcNow;
-            Id = Guid.NewGuid();
+            PayloadId = Guid.NewGuid();
             Key = key;
             State = PayloadState.Created;
             RetryCount = 0;
@@ -90,7 +91,7 @@ public Payload(string key, string correlationId, uint timeout)
 
         public void Add(FileStorageMetadata value)
         {
-            Guard.Against.Null(value, nameof(value));
+            Guard.Against.Null(value);
 
             Files.Add(value);
             _lastReceived.Reset();

src/Client.Common/ProblemException.cs

@@ -42,7 +42,7 @@ public override void GetObjectData(SerializationInfo info, StreamingContext cont
         {
             if (info == null)
             {
-                throw new ArgumentNullException("info");
+                throw new ArgumentNullException(nameof(info));
             }
 
             info.AddValue(nameof(ProblemDetails), ProblemDetails, typeof(ProblemDetails));

src/Common/ExtensionMethods.cs

@@ -73,7 +73,7 @@ public static string RemoveInvalidPathChars(this string input)
         /// <returns></returns>
         public static async Task<bool> Post<TInput>(this ActionBlock<TInput> actionBlock, TInput input, TimeSpan delay)
         {
-            await Task.Delay(delay);
+            await Task.Delay(delay).ConfigureAwait(false);
             return actionBlock.Post(input);
         }
     }

src/Common/Test/ExtensionMethodsTest.cs

@@ -90,7 +90,7 @@ public async Task GivenAnActionBlock_WhenPostWIithDelayIsCalled_ExpectADelayBefo
             });
 
             stopwatch.Start();
-            await actionBlock.Post(input, delay);
+            await actionBlock.Post(input, delay).ConfigureAwait(false);
         }
     }
 }

src/Configuration/Monai.Deploy.InformaticsGateway.Configuration.csproj

@@ -30,7 +30,7 @@
     </PackageReference>
     <PackageReference Include="Microsoft.Extensions.Logging.Abstractions" Version="6.0.2" />
     <PackageReference Include="Microsoft.Extensions.Options" Version="6.0.0" />
-    <PackageReference Include="Monai.Deploy.Messaging" Version="0.1.11" />
+    <PackageReference Include="Monai.Deploy.Messaging" Version="0.1.17-rc0020" />
     <PackageReference Include="Monai.Deploy.Storage" Version="0.2.10" />
     <PackageReference Include="System.IO.Abstractions" Version="17.2.3" />
   </ItemGroup>

src/Database/Api/DatabaseException.cs

@@ -0,0 +1,40 @@
+/*
+ * 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 System.Runtime.Serialization;
+
+namespace Monai.Deploy.InformaticsGateway.Database.Api
+{
+    [Serializable]
+    public class DatabaseException : Exception
+    {
+        public DatabaseException()
+        {
+        }
+
+        public DatabaseException(string? message) : base(message)
+        {
+        }
+
+        public DatabaseException(string? message, Exception? innerException) : base(message, innerException)
+        {
+        }
+
+        protected DatabaseException(SerializationInfo info, StreamingContext context) : base(info, context)
+        {
+        }
+    }
+}

src/Database/Api/Log.9000.cs

@@ -1,4 +1,4 @@
-/*
+/*
  * Copyright 2022 MONAI Consortium
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
@@ -16,35 +16,44 @@
 
 using Microsoft.Extensions.Logging;
 
-namespace Monai.Deploy.InformaticsGateway.Database.EntityFramework.Logging
+namespace Monai.Deploy.InformaticsGateway.Database.Api.Logging
 {
     public static partial class Log
     {
-        [LoggerMessage(EventId = 9100, Level = LogLevel.Error, Message = "Error performing database action. Waiting {timespan} before next retry. Retry attempt {retryCount}...")]
+        [LoggerMessage(EventId = 9000, Level = LogLevel.Error, Message = "Error adding item {type} to the database.")]
+        public static partial void ErrorAddItem(this ILogger logger, string @type, Exception ex);
+
+        [LoggerMessage(EventId = 9001, Level = LogLevel.Error, Message = "Error updating item {type} in the database.")]
+        public static partial void ErrorUpdateItem(this ILogger logger, string @type, Exception ex);
+
+        [LoggerMessage(EventId = 9002, Level = LogLevel.Error, Message = "Error deleting item {type} from the database.")]
+        public static partial void ErrorDeleteItem(this ILogger logger, string @type, Exception ex);
+
+        [LoggerMessage(EventId = 9003, Level = LogLevel.Error, Message = "Error performing database action. Waiting {timespan} before next retry. Retry attempt {retryCount}...")]
         public static partial void DatabaseErrorRetry(this ILogger logger, TimeSpan timespan, int retryCount, Exception ex);
 
-        [LoggerMessage(EventId = 9101, Level = LogLevel.Debug, Message = "Storage metadata saved to the database.")]
+        [LoggerMessage(EventId = 9004, Level = LogLevel.Debug, Message = "Storage metadata saved to the database.")]
         public static partial void StorageMetadataSaved(this ILogger logger);
 
-        [LoggerMessage(EventId = 9102, Level = LogLevel.Error, Message = "Error querying pending inference request.")]
+        [LoggerMessage(EventId = 9005, Level = LogLevel.Error, Message = "Error querying pending inference request.")]
         public static partial void ErrorQueryingForPendingInferenceRequest(this ILogger logger, Exception ex);
 
-        [LoggerMessage(EventId = 9103, Level = LogLevel.Debug, Message = "Inference request saved.")]
+        [LoggerMessage(EventId = 9006, Level = LogLevel.Debug, Message = "Inference request saved.")]
         public static partial void InferenceRequestSaved(this ILogger logger);
 
-        [LoggerMessage(EventId = 9104, Level = LogLevel.Warning, Message = "Exceeded maximum retries.")]
+        [LoggerMessage(EventId = 9007, Level = LogLevel.Warning, Message = "Exceeded maximum retries.")]
         public static partial void InferenceRequestUpdateExceededMaximumRetries(this ILogger logger);
 
-        [LoggerMessage(EventId = 9105, Level = LogLevel.Information, Message = "Failed to process inference request, will retry later.")]
+        [LoggerMessage(EventId = 9008, Level = LogLevel.Information, Message = "Failed to process inference request, will retry later.")]
         public static partial void InferenceRequestUpdateRetryLater(this ILogger logger);
 
-        [LoggerMessage(EventId = 9106, Level = LogLevel.Debug, Message = "Updating request {transactionId} to InProgress.")]
+        [LoggerMessage(EventId = 9009, Level = LogLevel.Debug, Message = "Updating request {transactionId} to InProgress.")]
         public static partial void InferenceRequestSetToInProgress(this ILogger logger, string transactionId);
 
-        [LoggerMessage(EventId = 9107, Level = LogLevel.Debug, Message = "Updating inference request.")]
+        [LoggerMessage(EventId = 9010, Level = LogLevel.Debug, Message = "Updating inference request.")]
         public static partial void InferenceRequestUpdateState(this ILogger logger);
 
-        [LoggerMessage(EventId = 9108, Level = LogLevel.Information, Message = "Inference request updated.")]
+        [LoggerMessage(EventId = 9011, Level = LogLevel.Information, Message = "Inference request updated.")]
         public static partial void InferenceRequestUpdated(this ILogger logger);
     }
 }

src/Database/EntityFramework/Logging/Log.9100.cs renamed to src/Database/Api/Logging/Log.9000.cs

@@ -46,7 +46,7 @@ public interface IStorageMetadataRepository
         /// Gets all storage metadata objects associated with the correlation ID.
         /// </summary>
         /// <param name="correlationId">Correlation ID</param>
-        Task<IList<FileStorageMetadata?>> GetFileStorageMetdadataAsync(string correlationId, CancellationToken cancellationToken = default);
+        Task<IList<FileStorageMetadata>> GetFileStorageMetdadataAsync(string correlationId, CancellationToken cancellationToken = default);
 
         /// <summary>
         /// Gets the specified storage metadata object.