gh-235 Add support for mongodb

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

Author: mocsharp

src/Api/BaseApplicationEntity.cs

@@ -23,8 +23,11 @@ namespace Monai.Deploy.InformaticsGateway.Api
     /// <remarks>
     /// * [Application Entity](http://www.otpedia.com/entryDetails.cfm?id=137)
     /// </remarks>
-    public class BaseApplicationEntity
+    public class BaseApplicationEntity : DatabaseEntityBase
     {
+        /// <inheritdoc/>
+        public override string Id { get => Name; set => Name = value; }
+
         /// <summary>
         /// Gets or sets the unique name used to identify a DICOM application entity.
         /// This value must be unique.

src/Api/IDatabaseEntity.cs

@@ -0,0 +1,42 @@
+/*
+ * 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;
+using MongoDB.Bson.Serialization.Attributes;
+
+namespace Monai.Deploy.InformaticsGateway.Api
+{
+    public interface IDatabaseEntity
+    {
+        /// <summary>
+        /// Gets or sets the internal object identifier.
+        /// </summary>
+        [BsonId]
+        string Id { get; set; }
+
+        /// <summary>
+        /// Gets or sets the date time object created.
+        /// </summary>
+        DateTimeOffset DateTimeCreated { get; }
+    }
+
+    public abstract class DatabaseEntityBase : IDatabaseEntity
+    {
+        public abstract string Id { get; set; }
+
+        public DateTimeOffset DateTimeCreated { get; set; } = DateTimeOffset.UtcNow;
+    }
+}

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

@@ -32,11 +32,15 @@
     <PackageReference Include="Microsoft.EntityFrameworkCore.Abstractions" Version="6.0.10" />
     <PackageReference Include="Monai.Deploy.Messaging" Version="0.1.9" />
     <PackageReference Include="Monai.Deploy.Storage" Version="0.2.10" />
+    <PackageReference Include="MongoDB.Bson" Version="2.18.0" />
   </ItemGroup>
 
   <ItemGroup>
+    <Compile Remove="MessageBroker\**" />
     <Compile Remove="Test\**" />
+    <EmbeddedResource Remove="MessageBroker\**" />
     <EmbeddedResource Remove="Test\**" />
+    <None Remove="MessageBroker\**" />
     <None Remove="Test\**" />
   </ItemGroup>
 
@@ -47,8 +51,4 @@
   <ItemGroup>
     <ProjectReference Include="..\Common\Monai.Deploy.InformaticsGateway.Common.csproj" />
   </ItemGroup>
-
-  <ItemGroup>
-    <Folder Include="MessageBroker\" />
-  </ItemGroup>
 </Project>

src/Api/MonaiApplicationEntity.cs

@@ -44,8 +44,11 @@ namespace Monai.Deploy.InformaticsGateway.Api
     /// }
     /// </code>
     /// </example>
-    public class MonaiApplicationEntity
+    public class MonaiApplicationEntity : DatabaseEntityBase
     {
+        /// <inheritdoc/>
+        public override string Id { get => Name; set => Name = value; }
+
         /// <summary>
         /// Gets or sets the name of a MONAI DICOM application entity.
         /// This value must be unique.

src/Api/Rest/InferenceRequest.cs

@@ -76,8 +76,11 @@ public enum InferenceRequestState
     /// <para><c>inputMetadata></c> is required.</para>
     /// <para><c>inputResources></c> is required.</para>
     /// </remarks>
-    public class InferenceRequest
+    public class InferenceRequest : DatabaseEntityBase
     {
+        /// <inheritdoc/>
+        public override string Id { get => InferenceRequestId; set => InferenceRequestId = value; }
+
         /// <summary>
         /// Gets or set the transaction ID of a request.
         /// </summary>
@@ -124,7 +127,7 @@ public class InferenceRequest
         /// <summary>
         /// Unique identity for the request.
         /// </summary>
-        public Guid InferenceRequestId { get; set; } = Guid.NewGuid();
+        public string InferenceRequestId { get; set; } = Guid.NewGuid().ToString();
 
         /// <summary>
         /// Internal use only - get or sets the state of a inference request.

src/Api/Storage/Payload.cs

@@ -22,7 +22,7 @@
 
 namespace Monai.Deploy.InformaticsGateway.Api.Storage
 {
-    public class Payload : IDisposable
+    public class Payload : DatabaseEntityBase, IDisposable
     {
         public enum PayloadState
         {
@@ -46,14 +46,15 @@ public enum PayloadState
         private readonly Stopwatch _lastReceived;
         private bool _disposedValue;
 
-        public Guid Id { get; }
+        /// <inheritdoc/>
+        public override string Id { get => PayloadId.ToString(); set => PayloadId = Guid.Parse(value); }
+
+        public Guid PayloadId { get; set; }
 
         public uint Timeout { get; init; }
 
         public string Key { get; init; }
 
-        public DateTime DateTimeCreated { get; private set; }
-
         public int RetryCount { get; set; }
 
         public PayloadState State { get; set; }
@@ -66,7 +67,10 @@ public enum PayloadState
 
         public bool HasTimedOut { get => ElapsedTime().TotalSeconds >= Timeout; }
 
-        public TimeSpan Elapsed { get { return DateTime.UtcNow.Subtract(DateTimeCreated); } }
+        public TimeSpan Elapsed
+        {
+            get { return DateTimeOffset.UtcNow.Subtract(DateTimeCreated); }
+        }
 
         public string CallingAeTitle { get => Files.OfType<DicomFileStorageMetadata>().Select(p => p.CallingAeTitle).FirstOrDefault(); }
 
@@ -81,7 +85,7 @@ public Payload(string key, string correlationId, uint timeout)
 
             CorrelationId = correlationId;
             DateTimeCreated = DateTime.UtcNow;
-            Id = Guid.NewGuid();
+            Id = Guid.NewGuid().ToString();
             Key = key;
             State = PayloadState.Created;
             RetryCount = 0;

src/CLI/Commands/SourceCommand.cs

@@ -45,7 +45,6 @@ public SourceCommand() : base("src", "Configure DICOM sources")
             SetupListSourceCommand();
         }
 
-
         private void SetupListSourceCommand()
         {
             var listCommand = new Command("ls", "List all DICOM sources");
@@ -81,6 +80,7 @@ private void SetupAddSourceCommand()
 
             addCommand.Handler = CommandHandler.Create<SourceApplicationEntity, IHost, bool, CancellationToken>(AddSourceHandlerAsync);
         }
+
         private void SetupUpdateSourceCommand()
         {
             var addCommand = new Command("update", "Update a new DICOM source");
@@ -233,6 +233,7 @@ private async Task<int> AddSourceHandlerAsync(SourceApplicationEntity entity, IH
             }
             return ExitCodes.Success;
         }
+
         private async Task<int> UpdateSourceHandlerAsync(SourceApplicationEntity entity, IHost host, bool verbose, CancellationToken cancellationTokena)
         {
             Guard.Against.Null(entity, nameof(entity));

src/CLI/Test/DestinationCommandTest.cs

@@ -339,7 +339,6 @@ public async Task DstCEcho_Command_ConfigurationException()
             _logger.VerifyLoggingMessageBeginsWith("Please execute `testhost config init` to intialize Informatics Gateway.", LogLevel.Critical, Times.Once());
         }
 
-
         [Fact(DisplayName = "dst update command")]
         public async Task DstUpdate_Command()
         {

src/CLI/Test/SourceCommandTest.cs

@@ -346,6 +346,5 @@ public async Task SrcUpdate_Command_ConfigurationException()
 
             _logger.VerifyLoggingMessageBeginsWith("Please execute `testhost config init` to intialize Informatics Gateway.", LogLevel.Critical, Times.Once());
         }
-
     }
 }

src/Client/Test/AeTitleServiceTest.cs

@@ -422,7 +422,6 @@ public async Task CEcho()
 
             var exception = await Record.ExceptionAsync(async () => await service.CEcho(aet.Name, CancellationToken.None));
             Assert.Null(exception);
-
         }
 
         [Fact(DisplayName = "Destination - C-ECHO returns a problem")]

src/Configuration/StorageConfiguration.cs

@@ -43,7 +43,6 @@ public class StorageConfiguration : StorageServiceConfiguration
         [ConfigurationKeyName("bufferSize")]
         public int BufferSize { get; set; } = 128000;
 
-
         /// <summary>
         /// Gets or set the maximum memory buffer size in bytes with default to 30MiB.
         /// </summary>

src/Database/Api/IInformaticsGatewayRepository.cs

@@ -14,32 +14,29 @@
  * limitations under the License.
  */
 
-using Microsoft.EntityFrameworkCore.ChangeTracking;
+using System.Linq.Expressions;
+using Monai.Deploy.InformaticsGateway.Api;
 
 namespace Monai.Deploy.InformaticsGateway.Database.Api
 {
-    public interface IInformaticsGatewayRepository<T> where T : class
+    public interface IInformaticsGatewayRepository<T> where T : IDatabaseEntity
     {
         IQueryable<T> AsQueryable();
 
-        Task<T> FindAsync(params object[] keyValues);
+        Task<bool> AnyAsync(Expression<Func<T, bool>> filterExpression, CancellationToken cancellationToken = default);
 
-        Task<int> SaveChangesAsync(CancellationToken cancellationToken = default);
+        Task<T?> FindByIdAsync(string key, CancellationToken cancellationToken = default);
 
-        Task<List<T>> ToListAsync();
+        Task<T?> FirstOrDefaultAsync(Expression<Func<T, bool>> filterExpression, CancellationToken cancellationToken = default);
 
-        EntityEntry<T> Update(T entity);
+        Task<List<T>> ToListAsync(CancellationToken cancellationToken = default);
 
-        EntityEntry<T> Remove(T entity);
+        Task<T> AddAsync(T entity, CancellationToken cancellationToken = default);
 
-        void RemoveRange(params T[] entities);
+        Task<T> UpdateAsync(T entity, CancellationToken cancellationToken = default);
 
-        Task<EntityEntry<T>> AddAsync(T item, CancellationToken cancellationToken = default);
+        Task<T> RemoveAsync(T entity, CancellationToken cancellationToken = default);
 
-        T FirstOrDefault(Func<T, bool> p);
-
-        void Detach(T job);
-
-        bool Any(Func<T, bool> p);
+        Task RemoveRangeAsync(CancellationToken cancellationToken = default, params T[] entities);
     }
 }

src/Database/Api/Log.9000.cs

@@ -0,0 +1,32 @@
+/*
+ * 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 Microsoft.Extensions.Logging;
+
+namespace Monai.Deploy.InformaticsGateway.Database.Api
+{
+    public static partial class Log
+    {
+        [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);
+    }
+}

src/Database/EntityFramework/Configuration/SR.cs renamed to src/Database/Api/SR.cs

@@ -15,14 +15,13 @@
  * limitations under the License.
  */
 
-namespace Monai.Deploy.InformaticsGateway.Database.EntityFramework.Configurations
+namespace Monai.Deploy.InformaticsGateway.Database.Api
 {
     public static class SR
     {
         /// <summary>
         /// Name of the key for retrieve database connection string.
         /// </summary>
         public const string DatabaseConnectionStringKey = "InformaticsGatewayDatabase";
-
     }
 }

src/Database/Api/StorageMetadataWrapper.cs

@@ -17,23 +17,27 @@
 using System.Text.Json;
 using System.Text.Json.Serialization;
 using Ardalis.GuardClauses;
+using Monai.Deploy.InformaticsGateway.Api;
 using Monai.Deploy.InformaticsGateway.Api.Storage;
 
 namespace Monai.Deploy.InformaticsGateway.Database.Api
 {
-    public class StorageMetadataWrapper
+    public class StorageMetadataWrapper : DatabaseEntityBase
     {
+        /// <inheritdoc/>
+        public override string Id { get => Identity; set => Identity = value; }
+
         [JsonPropertyName("correlationId")]
-        public string CorrelationId { get; set; }
+        public string CorrelationId { get; set; } = string.Empty;
 
         [JsonPropertyName("identity")]
-        public string Identity { get; set; }
+        public string Identity { get; set; } = string.Empty;
 
         [JsonPropertyName("value")]
-        public string Value { get; set; }
+        public string Value { get; set; } = string.Empty;
 
         [JsonPropertyName("typeName")]
-        public string TypeName { get; set; }
+        public string TypeName { get; set; } = string.Empty;
 
         [JsonPropertyName("isUploaded")]
         public bool IsUploaded { get; set; }
@@ -43,7 +47,7 @@ private StorageMetadataWrapper()
 
         public StorageMetadataWrapper(FileStorageMetadata metadata)
         {
-            Guard.Against.Null(metadata, nameof(metadata));
+            Guard.Against.Null(metadata);
 
             CorrelationId = metadata.CorrelationId;
             Identity = metadata.Id;
@@ -52,14 +56,14 @@ public StorageMetadataWrapper(FileStorageMetadata metadata)
 
         public void Update(FileStorageMetadata metadata)
         {
-            Guard.Against.Null(metadata, nameof(metadata));
+            Guard.Against.Null(metadata);
 
             IsUploaded = metadata.IsUploaded;
             Value = JsonSerializer.Serialize<object>(metadata);
-            TypeName = metadata.GetType().AssemblyQualifiedName;
+            TypeName = metadata.GetType().AssemblyQualifiedName!;
         }
 
-        public FileStorageMetadata GetObject()
+        public FileStorageMetadata? GetObject()
         {
             var type = Type.GetType(TypeName, true);
             return JsonSerializer.Deserialize(Value, type) as FileStorageMetadata;