Refactor database projects to support multiple database types (#237)

* gh-235 Refactor sqlite support to new projects
* Set DB type for integration test

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

Author: mocsharp

.licenserc.yaml

@@ -30,7 +30,7 @@ header:
     - 'src/.sonarlint/**'
     - 'src/coverlet.runsettings'
     - 'src/Monai.Deploy.InformaticsGateway.sln'
-    - 'src/Database/Migrations/**'
+    - 'src/Database/EntityFramework/Migrations/**'
     - 'demos/**/.env/**'
     - 'demos/**/*.txt'
     - 'doc/dependency_decisions.yml'

docs/compliance/third-party-licenses.md

@@ -24,11 +24,6 @@ namespace Monai.Deploy.InformaticsGateway.Configuration
     /// </summary>
     public class InformaticsGatewayConfiguration
     {
-        /// <summary>
-        /// Name of the key for retrieve database connection string.
-        /// </summary>
-        public const string DatabaseConnectionStringKey = "InformaticsGatewayDatabase";
-
         /// <summary>
         /// Represents the <c>dicom</c> section of the configuration file.
         /// </summary>

src/Configuration/InformaticsGatewayConfiguration.cs

@@ -1,6 +1,5 @@
 /*
- * Copyright 2021-2022 MONAI Consortium
- * Copyright 2019-2021 NVIDIA Corporation
+ * 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.
@@ -15,9 +14,12 @@
  * limitations under the License.
  */
 
-namespace Monai.Deploy.InformaticsGateway.Repositories
+using Microsoft.Extensions.Hosting;
+
+namespace Monai.Deploy.InformaticsGateway.Database.Api
 {
-    public class StorageObjectsinferenceRequest
+    public interface IDatabaseMigrationManager
     {
+        IHost Migrate(IHost host);
     }
-}
+}

src/InformaticsGateway/Repositories/StorageObjectsinferenceRequest.cs renamed to src/Database/Api/IDatabaseMigrationManager.cs

@@ -14,14 +14,9 @@
  * limitations under the License.
  */
 
-using System;
-using System.Collections.Generic;
-using System.Linq;
-using System.Threading;
-using System.Threading.Tasks;
 using Microsoft.EntityFrameworkCore.ChangeTracking;
 
-namespace Monai.Deploy.InformaticsGateway.Repositories
+namespace Monai.Deploy.InformaticsGateway.Database.Api
 {
     public interface IInformaticsGatewayRepository<T> where T : class
     {

src/InformaticsGateway/Repositories/IInformaticsGatewayRepository.cs renamed to src/Database/Api/IInformaticsGatewayRepository.cs

@@ -0,0 +1,40 @@
+<!--
+  ~ Copyright 2021-2022 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.
+-->
+
+<Project Sdk="Microsoft.NET.Sdk">
+
+  <PropertyGroup>
+    <RootNamespace>Monai.Deploy.InformaticsGateway.Database.Repositories</RootNamespace>
+    <TargetFramework>net6.0</TargetFramework>
+    <ImplicitUsings>enable</ImplicitUsings>
+    <Nullable>enable</Nullable>
+  </PropertyGroup>
+
+  <ItemGroup>
+    <Compile Remove="Test\**" />
+    <EmbeddedResource Remove="Test\**" />
+    <None Remove="Test\**" />
+  </ItemGroup>
+
+  <ItemGroup>
+    <PackageReference Include="Microsoft.EntityFrameworkCore" Version="6.0.10" />
+  </ItemGroup>
+
+  <ItemGroup>
+    <ProjectReference Include="..\..\Api\Monai.Deploy.InformaticsGateway.Api.csproj" />
+  </ItemGroup>
+
+</Project>

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

@@ -19,7 +19,7 @@
 using Ardalis.GuardClauses;
 using Monai.Deploy.InformaticsGateway.Api.Storage;
 
-namespace Monai.Deploy.InformaticsGateway.Database
+namespace Monai.Deploy.InformaticsGateway.Database.Api
 {
     public class StorageMetadataWrapper
     {
@@ -61,7 +61,7 @@ public void Update(FileStorageMetadata metadata)
 
         public FileStorageMetadata GetObject()
         {
-            var type = System.Type.GetType(TypeName, true);
+            var type = Type.GetType(TypeName, true);
             return JsonSerializer.Deserialize(Value, type) as FileStorageMetadata;
         }
     }

src/Database/StorageMetadataWrapper.cs renamed to src/Database/Api/StorageMetadataWrapper.cs

@@ -38,8 +38,8 @@
   </ItemGroup>
 
   <ItemGroup>
-    <ProjectReference Include="..\..\Api\Monai.Deploy.InformaticsGateway.Api.csproj" />
-    <ProjectReference Include="..\Monai.Deploy.InformaticsGateway.Database.csproj" />
+    <ProjectReference Include="..\..\..\Api\Monai.Deploy.InformaticsGateway.Api.csproj" />
+    <ProjectReference Include="..\Monai.Deploy.InformaticsGateway.Database.Api.csproj" />
   </ItemGroup>
 
 </Project>

src/Database/Test/Monai.Deploy.InformaticsGateway.Database.Test.csproj renamed to src/Database/Api/Test/Monai.Deploy.InformaticsGateway.Database.Api.Test.csproj

@@ -14,7 +14,9 @@
  * limitations under the License.
  */
 
+using Monai.Deploy.InformaticsGateway.Api.Rest;
 using Monai.Deploy.InformaticsGateway.Api.Storage;
+using Monai.Deploy.InformaticsGateway.Database.Api;
 
 namespace Monai.Deploy.InformaticsGateway.Database.Test
 {
@@ -27,7 +29,7 @@ public void GivenAFhirFileStorageMetadataObject_WhenInitializedWithStorageMetada
                 Guid.NewGuid().ToString(),
                 Guid.NewGuid().ToString(),
                 Guid.NewGuid().ToString(),
-                Api.Rest.FhirStorageFormat.Json);
+                FhirStorageFormat.Json);
             metadata.SetWorkflows("A", "B", "C");
 
             var wrapper = new StorageMetadataWrapper(metadata);

src/Database/Test/StorageMetadataWrapperTest.cs renamed to src/Database/Api/Test/StorageMetadataWrapperTest.cs

@@ -0,0 +1,52 @@
+/*
+ * 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.EntityFrameworkCore;
+using Microsoft.Extensions.Configuration;
+using Microsoft.Extensions.DependencyInjection;
+using Monai.Deploy.InformaticsGateway.Configuration;
+using Monai.Deploy.InformaticsGateway.Database.Api;
+using Monai.Deploy.InformaticsGateway.Database.EntityFramework;
+using Monai.Deploy.InformaticsGateway.Database.EntityFramework.Configurations;
+
+namespace Monai.Deploy.InformaticsGateway.Database
+{
+    public static class DatabaseManager
+    {
+        public static IServiceCollection ConfigureDatabase(this IServiceCollection services, IConfigurationSection? connectionStringConfigurationSection)
+        {
+            if (connectionStringConfigurationSection is null)
+            {
+                throw new ConfigurationException("No database connections found in configuration section 'ConnectionStrings'.");
+            }
+
+
+            var databaseType = connectionStringConfigurationSection["Type"];
+            switch (databaseType)
+            {
+                case "Sqlite":
+                    services.AddScoped<IDatabaseMigrationManager, EfDatabaseMigrationManager>();
+                    services.AddScoped(typeof(IInformaticsGatewayRepository<>), typeof(InformaticsGatewayRepository<>));
+                    services.AddDbContext<InformaticsGatewayContext>(
+                        options => options.UseSqlite(connectionStringConfigurationSection[SR.DatabaseConnectionStringKey]),
+                        ServiceLifetime.Transient);
+                    return services;
+                default:
+                    throw new ConfigurationException($"Unsupported database type defined: '{databaseType}'");
+            }
+        }
+    }
+}

src/Database/Test/Usings.cs renamed to src/Database/Api/Test/Usings.cs

@@ -0,0 +1,35 @@
+/*
+ * 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.DependencyInjection;
+using Microsoft.Extensions.Hosting;
+using Monai.Deploy.InformaticsGateway.Database.Api;
+
+namespace Monai.Deploy.InformaticsGateway.Database
+{
+    public static class DatabaseMigrationManager
+    {
+        public static IHost MigrateDatabase(this IHost host)
+        {
+            using (var scope = host.Services.CreateScope())
+            {
+                scope.ServiceProvider.GetRequiredService<IDatabaseMigrationManager>()?.Migrate(host);
+            }
+            return host;
+        }
+    }
+}
+

src/Database/DatabaseManager.cs

@@ -19,7 +19,7 @@
 using Microsoft.EntityFrameworkCore.Metadata.Builders;
 using Monai.Deploy.InformaticsGateway.Api;
 
-namespace Monai.Deploy.InformaticsGateway.Database
+namespace Monai.Deploy.InformaticsGateway.Database.EntityFramework.Configurations
 {
     internal class DestinationApplicationEntityConfiguration : IEntityTypeConfiguration<DestinationApplicationEntity>
     {

src/Database/DatabaseMigrationManager.cs

@@ -25,7 +25,7 @@
 using Microsoft.EntityFrameworkCore.Metadata.Builders;
 using Monai.Deploy.InformaticsGateway.Api.Rest;
 
-namespace Monai.Deploy.InformaticsGateway.Database
+namespace Monai.Deploy.InformaticsGateway.Database.EntityFramework.Configurations
 {
     internal class InferenceRequestConfiguration : IEntityTypeConfiguration<InferenceRequest>
     {

src/Database/DestinationApplicationEntityConfiguration.cs renamed to src/Database/EntityFramework/Configuration/DestinationApplicationEntityConfiguration.cs

@@ -25,7 +25,7 @@
 using Microsoft.EntityFrameworkCore.Metadata.Builders;
 using Monai.Deploy.InformaticsGateway.Api;
 
-namespace Monai.Deploy.InformaticsGateway.Database
+namespace Monai.Deploy.InformaticsGateway.Database.EntityFramework.Configurations
 {
     internal class MonaiApplicationEntityConfiguration : IEntityTypeConfiguration<MonaiApplicationEntity>
     {

src/Database/InferenceRequestConfiguration.cs renamed to src/Database/EntityFramework/Configuration/InferenceRequestConfiguration.cs

@@ -24,7 +24,7 @@
 using Microsoft.EntityFrameworkCore.Metadata.Builders;
 using Monai.Deploy.InformaticsGateway.Api.Storage;
 
-namespace Monai.Deploy.InformaticsGateway.Database
+namespace Monai.Deploy.InformaticsGateway.Database.EntityFramework.Configurations
 {
     internal class PayloadConfiguration : IEntityTypeConfiguration<Payload>
     {

src/Database/MonaiApplicationEntityConfiguration.cs renamed to src/Database/EntityFramework/Configuration/MonaiApplicationEntityConfiguration.cs

@@ -0,0 +1,28 @@
+/*
+ * Copyright 2021-2022 MONAI Consortium
+ * Copyright 2019-2021 NVIDIA Corporation
+ *
+ * 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.
+ */
+
+namespace Monai.Deploy.InformaticsGateway.Database.EntityFramework.Configurations
+{
+    public static class SR
+    {
+        /// <summary>
+        /// Name of the key for retrieve database connection string.
+        /// </summary>
+        public const string DatabaseConnectionStringKey = "InformaticsGatewayDatabase";
+
+    }
+}

src/Database/PayloadConfiguration.cs renamed to src/Database/EntityFramework/Configuration/PayloadConfiguration.cs

@@ -18,7 +18,7 @@
 using Microsoft.EntityFrameworkCore;
 using Monai.Deploy.InformaticsGateway.Api;
 
-namespace Monai.Deploy.InformaticsGateway.Database
+namespace Monai.Deploy.InformaticsGateway.Database.EntityFramework.Configurations
 {
     internal class SourceApplicationEntityConfiguration : IEntityTypeConfiguration<SourceApplicationEntity>
     {

src/Database/EntityFramework/Configuration/SR.cs

@@ -17,8 +17,9 @@
 
 using Microsoft.EntityFrameworkCore;
 using Microsoft.EntityFrameworkCore.Metadata.Builders;
+using Monai.Deploy.InformaticsGateway.Database.Api;
 
-namespace Monai.Deploy.InformaticsGateway.Database
+namespace Monai.Deploy.InformaticsGateway.Database.EntityFramework.Configurations
 {
     internal class StorageMetadataWrapperEntityConfiguration : IEntityTypeConfiguration<StorageMetadataWrapper>
     {

src/Database/SourceApplicationEntityConfiguration.cs renamed to src/Database/EntityFramework/Configuration/SourceApplicationEntityConfiguration.cs

@@ -0,0 +1,48 @@
+/*
+ * 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.EntityFrameworkCore;
+using Microsoft.Extensions.DependencyInjection;
+using Microsoft.Extensions.Hosting;
+using Microsoft.Extensions.Logging;
+using Monai.Deploy.InformaticsGateway.Database.Api;
+
+namespace Monai.Deploy.InformaticsGateway.Database.EntityFramework
+{
+    public class EfDatabaseMigrationManager : IDatabaseMigrationManager
+    {
+        public IHost Migrate(IHost host)
+        {
+            using (var scope = host.Services.CreateScope())
+            {
+                using (var dbContext = scope.ServiceProvider.GetRequiredService<InformaticsGatewayContext>())
+                {
+                    try
+                    {
+                        dbContext.Database.Migrate();
+                    }
+                    catch (Exception ex)
+                    {
+                        var logger = scope.ServiceProvider.GetService<ILogger>();
+                        logger?.Log(LogLevel.Critical, "Failed to migrate database", ex);
+                        throw;
+                    }
+                }
+            }
+            return host;
+        }
+    }
+}

src/Database/StorageMetadataWrapperEntityConfiguration.cs renamed to src/Database/EntityFramework/Configuration/StorageMetadataWrapperEntityConfiguration.cs

@@ -18,8 +18,9 @@
 using Microsoft.EntityFrameworkCore.Diagnostics;
 using Microsoft.Extensions.Logging;
 using Monai.Deploy.InformaticsGateway.Api;
+using Monai.Deploy.InformaticsGateway.Database.EntityFramework.Configurations;
 
-namespace Monai.Deploy.InformaticsGateway.Database
+namespace Monai.Deploy.InformaticsGateway.Database.EntityFramework
 {
     public class InformaticsGatewayContext : DbContext
     {