refactoring and more tests

neildsouth · neildsouth · commit e6e6c3067942 · 2023-08-11T17:37:48.000+01:00
Signed-off-by: Neil South &lt;neil.south@answerdigital.com&gt;
diff --git a/src/Api/Storage/RemoteAppExecution.cs b/src/Api/Storage/RemoteAppExecution.cs
@@ -35,5 +35,12 @@ public class RemoteAppExecution
         public List<string> Files { get; set; } = new();
         public FileExportStatus Status { get; set; }
         public Dictionary<string, string> OriginalValues { get; set; } = new();
+        public Dictionary<string, string> ProxyValues { get; set; } = new();
+    }
+    public class RemoteAppExecutionTest
+    {
+        [JsonPropertyName("_id")]
+        public string Id { get; set; } = default!;
+        public DateTime RequestTime { get; set; } = DateTime.UtcNow;
     }
 }
diff --git a/src/Database/EntityFramework/Configuration/RemoteAppExecutionConfiguration.cs b/src/Database/EntityFramework/Configuration/RemoteAppExecutionConfiguration.cs
@@ -0,0 +1,63 @@
+/*
+ * 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.
+ */
+
+using System.Text.Json;
+using System.Text.Json.Serialization;
+using Microsoft.EntityFrameworkCore;
+using Microsoft.EntityFrameworkCore.ChangeTracking;
+using Microsoft.EntityFrameworkCore.Metadata.Builders;
+using Monai.Deploy.InformaticsGateway.Api.Storage;
+
+namespace Monai.Deploy.InformaticsGateway.Database.EntityFramework.Configuration
+{
+#pragma warning disable CS8604, CS8603
+
+    internal class RemoteAppExecutionConfiguration : IEntityTypeConfiguration<RemoteAppExecution>
+    {
+        public void Configure(EntityTypeBuilder<RemoteAppExecution> builder)
+        {
+            var jsonSerializerSettings = new JsonSerializerOptions
+            {
+                DefaultIgnoreCondition = JsonIgnoreCondition.WhenWritingNull
+            };
+
+            builder.HasKey(j => j.Id);
+
+            builder.Property(j => j.OutgoingUid).IsRequired();
+            builder.Property(j => j.ExportTaskId).IsRequired();
+            //builder.Property(j => j.Status).IsRequired();
+            builder.Property(j => j.CorrelationId).IsRequired();
+            builder.Property(j => j.OriginalValues)
+                .HasConversion(
+                        v => JsonSerializer.Serialize(v, jsonSerializerSettings),
+                        v => JsonSerializer.Deserialize<Dictionary<string, string>>(v, jsonSerializerSettings));
+            builder.Property(j => j.ProxyValues)
+                .HasConversion(
+                        v => JsonSerializer.Serialize(v, jsonSerializerSettings),
+                        v => JsonSerializer.Deserialize<Dictionary<string, string>>(v, jsonSerializerSettings));
+
+            builder.Property(j => j.Files)
+                .HasConversion(
+                        v => JsonSerializer.Serialize(v, jsonSerializerSettings),
+                        v => JsonSerializer.Deserialize<List<string>>(v, jsonSerializerSettings));
+
+            builder.HasIndex(p => p.OutgoingUid, "idx_outgoing_key");
+
+        }
+    }
+
+#pragma warning restore CS8604, CS8603
+}
diff --git a/src/Database/EntityFramework/InformaticsGatewayContext.cs b/src/Database/EntityFramework/InformaticsGatewayContext.cs
@@ -40,6 +40,7 @@ public InformaticsGatewayContext(DbContextOptions<InformaticsGatewayContext> opt
         public virtual DbSet<Payload> Payloads { get; set; }
         public virtual DbSet<StorageMetadataWrapper> StorageMetadataWrapperEntities { get; set; }
         public virtual DbSet<DicomAssociationInfo> DicomAssociationHistories { get; set; }
+        public virtual DbSet<RemoteAppExecution> RemoteAppExecutions { get; set; }
 
         protected override void OnModelCreating(ModelBuilder modelBuilder)
         {
@@ -52,6 +53,7 @@ protected override void OnModelCreating(ModelBuilder modelBuilder)
             modelBuilder.ApplyConfiguration(new PayloadConfiguration());
             modelBuilder.ApplyConfiguration(new StorageMetadataWrapperEntityConfiguration());
             modelBuilder.ApplyConfiguration(new DicomAssociationInfoConfiguration());
+            modelBuilder.ApplyConfiguration(new RemoteAppExecutionConfiguration());
         }
 
         protected override void OnConfiguring(DbContextOptionsBuilder optionsBuilder)
diff --git a/src/Database/EntityFramework/Repositories/RemoteAppExecutionRepository.cs b/src/Database/EntityFramework/Repositories/RemoteAppExecutionRepository.cs
@@ -31,7 +31,7 @@ namespace Monai.Deploy.InformaticsGateway.Database.EntityFramework.Repositories
 {
     public class RemoteAppExecutionRepository : IRemoteAppExecutionRepository, IDisposable
     {
-        private readonly ILogger<PayloadRepository> _logger;
+        private readonly ILogger<RemoteAppExecutionRepository> _logger;
         private readonly IServiceScope _scope;
         private readonly InformaticsGatewayContext _informaticsGatewayContext;
         private readonly AsyncRetryPolicy _retryPolicy;
@@ -44,7 +44,7 @@ public class RemoteAppExecutionRepository : IRemoteAppExecutionRepository, IDisp
 
         public RemoteAppExecutionRepository(
             IServiceScopeFactory serviceScopeFactory,
-            ILogger<PayloadRepository> logger,
+            ILogger<RemoteAppExecutionRepository> logger,
             IOptions<InformaticsGatewayConfiguration> options)
         {
             Guard.Against.Null(serviceScopeFactory, nameof(serviceScopeFactory));
diff --git a/src/Database/EntityFramework/Test/RemoteAppRepositoryTest.cs b/src/Database/EntityFramework/Test/RemoteAppRepositoryTest.cs
@@ -0,0 +1,124 @@
+﻿/*
+ * 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;
+using Monai.Deploy.InformaticsGateway.Api.Storage;
+using Monai.Deploy.InformaticsGateway.Configuration;
+using Monai.Deploy.InformaticsGateway.Database.EntityFramework.Repositories;
+using Monai.Deploy.InformaticsGateway.Database.EntityFramework.Test;
+using Moq;
+namespace Monai.Deploy.InformaticsGateway.Database.MongoDB.Integration.Test
+{
+    [Collection("SqliteDatabase")]
+    public class RemoteAppRepositoryTest
+    {
+        private readonly SqliteDatabaseFixture _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(SqliteDatabaseFixture databaseFixture)
+        {
+
+            _databaseFixture = databaseFixture ?? throw new ArgumentNullException(nameof(databaseFixture));
+
+            _serviceScopeFactory = new Mock<IServiceScopeFactory>();
+            _logger = new Mock<ILogger<RemoteAppExecutionRepository>>();
+            _options = Microsoft.Extensions.Options.Options.Create(new InformaticsGatewayConfiguration());
+
+            _serviceScope = new Mock<IServiceScope>();
+            var services = new ServiceCollection();
+            services.AddScoped(p => _logger.Object);
+            services.AddScoped(p => databaseFixture.DatabaseContext);
+
+            _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);
+            databaseFixture.DatabaseContext.Set<RemoteAppExecution>();
+            databaseFixture.DatabaseContext.SaveChanges();
+        }
+
+        [Fact]
+        public async Task GivenAexecution_WhenAddingToDatabase_ExpectItToBeSaved()
+        {
+            var outgoingUid = Guid.NewGuid().ToString();
+            var dataset = new DicomDataset();
+            var date = new DateTime(
+                DateTime.Now.Year,
+                DateTime.Now.Month,
+                DateTime.Now.Day,
+                DateTime.Now.Hour,
+                DateTime.Now.Minute,
+                DateTime.Now.Second).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" }
+                },
+                ProxyValues = new Dictionary<string, string> {
+                    { DicomTag.StudyInstanceUID.ToString(), "StudyInstanceUID" },
+                    { DicomTag.SeriesInstanceUID.ToString(), "SeriesInstanceUID" }
+                }
+            };
+
+
+            var store = new RemoteAppExecutionRepository(_serviceScopeFactory.Object, _logger.Object, _options);
+            await store.AddAsync(execution).ConfigureAwait(false);
+
+            var actual = await store.GetAsync(execution.OutgoingUid).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(execution.ProxyValues, actual!.ProxyValues);
+            Assert.Equal(2, actual!.OriginalValues.Count);
+
+            await store.RemoveAsync(execution.OutgoingUid).ConfigureAwait(false);
+
+            actual = await _databaseFixture.DatabaseContext.Set<RemoteAppExecution>().FirstOrDefaultAsync(p => p.OutgoingUid == execution.OutgoingUid).ConfigureAwait(false);
+            Assert.Null(actual);
+        }
+    }
+}
diff --git a/src/Database/MongoDB/Integration.Test/RemoteAppRepositoryTest.cs b/src/Database/MongoDB/Integration.Test/RemoteAppRepositoryTest.cs
@@ -42,6 +42,7 @@ public class RemoteAppRepositoryTest
 
         public RemoteAppRepositoryTest(MongoDatabaseFixture databaseFixture)
         {
+
             _databaseFixture = databaseFixture ?? throw new ArgumentNullException(nameof(databaseFixture));
 
             _serviceScopeFactory = new Mock<IServiceScopeFactory>();
@@ -66,7 +67,13 @@ 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 date = new DateTime(
+                DateTime.Now.Year,
+                DateTime.Now.Month,
+                DateTime.Now.Day,
+                DateTime.Now.Hour,
+                DateTime.Now.Minute,
+                DateTime.Now.Second).ToUniversalTime();
 
             var execution = new RemoteAppExecution
             {
@@ -79,6 +86,10 @@ public async Task GivenAexecution_WhenAddingToDatabase_ExpectItToBeSaved()
                 OriginalValues = new Dictionary<string, string> {
                     { DicomTag.StudyInstanceUID.ToString(), "StudyInstanceUID" },
                     { DicomTag.SeriesInstanceUID.ToString(), "SeriesInstanceUID" }
+                },
+                ProxyValues = new Dictionary<string, string> {
+                    { DicomTag.StudyInstanceUID.ToString(), "StudyInstanceUID" },
+                    { DicomTag.SeriesInstanceUID.ToString(), "SeriesInstanceUID" }
                 }
             };
 
@@ -87,7 +98,8 @@ public async Task GivenAexecution_WhenAddingToDatabase_ExpectItToBeSaved()
             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);
+
+            var actual = await store.GetAsync(execution.OutgoingUid).ConfigureAwait(false);
 
             Task.Delay(1000).Wait();
             Assert.NotNull(actual);
@@ -100,7 +112,13 @@ public async Task GivenAexecution_WhenAddingToDatabase_ExpectItToBeSaved()
             Assert.Equal(execution.StudyUid, actual!.StudyUid);
             Assert.Equal(execution.RequestTime, actual!.RequestTime);
             Assert.Equal(execution.OriginalValues, actual!.OriginalValues);
+            Assert.Equal(execution.ProxyValues, actual!.ProxyValues);
             Assert.Equal(2, actual!.OriginalValues.Count);
+
+            await store.RemoveAsync(execution.OutgoingUid).ConfigureAwait(false);
+
+            actual = await collection.Find(p => p.OutgoingUid == execution.OutgoingUid).FirstOrDefaultAsync().ConfigureAwait(false);
+            Assert.Null(actual);
         }
     }
 }
diff --git a/src/Database/MongoDB/Repositories/RemoteAppExecutionRepository.cs b/src/Database/MongoDB/Repositories/RemoteAppExecutionRepository.cs
@@ -61,11 +61,17 @@ public RemoteAppExecutionRepository(IServiceScopeFactory serviceScopeFactory,
 
         private void CreateIndexes()
         {
-            var options = new CreateIndexOptions { Unique = true, ExpireAfter = TimeSpan.FromDays(7), Name = "RequestTime" };
+            var options = new CreateIndexOptions { Unique = true };
             var indexDefinitionState = Builders<RemoteAppExecution>.IndexKeys.Ascending(_ => _.OutgoingUid);
             var indexModel = new CreateIndexModel<RemoteAppExecution>(indexDefinitionState, options);
 
             _collection.Indexes.CreateOne(indexModel);
+
+            options = new CreateIndexOptions { ExpireAfter = TimeSpan.FromDays(7), Name = "RequestTime" };
+            indexDefinitionState = Builders<RemoteAppExecution>.IndexKeys.Ascending(_ => _.RequestTime);
+            indexModel = new CreateIndexModel<RemoteAppExecution>(indexDefinitionState, options);
+
+            _collection.Indexes.CreateOne(indexModel);
         }
 
         public async Task<bool> AddAsync(RemoteAppExecution item, CancellationToken cancellationToken = default)
diff --git a/src/InformaticsGateway/Common/IDicomToolkit.cs b/src/InformaticsGateway/Common/IDicomToolkit.cs
@@ -17,6 +17,7 @@
 
 using System;
 using System.IO;
+using System.Linq;
 using System.Text.RegularExpressions;
 using System.Threading.Tasks;
 using FellowOakDicom;
@@ -32,5 +33,48 @@ public interface IDicomToolkit
         StudySerieSopUids GetStudySeriesSopInstanceUids(DicomFile dicomFile);
 
         static DicomTag GetDicomTagByName(string tag) => DicomDictionary.Default[tag] ?? DicomDictionary.Default[Regex.Replace(tag, @"\s+", "", RegexOptions.None, TimeSpan.FromSeconds(1))];
+
+        static DicomTag[] GetTagArrayFromStringArray(string values)
+        {
+            var names = values.Split(',', StringSplitOptions.RemoveEmptyEntries | StringSplitOptions.TrimEntries);
+            return names.Select(n => IDicomToolkit.GetDicomTagByName(n)).ToArray();
+        }
+
+        static T GetTagProxyValue<T>(DicomTag tag) where T : class
+        {
+            // partial implementation for now see
+            // https://dicom.nema.org/dicom/2013/output/chtml/part05/sect_6.2.html
+            // for full list
+            var output = "";
+            switch (tag.DictionaryEntry.ValueRepresentations[0].Code)
+            {
+                case "UI":
+                case "LO":
+                case "LT":
+                {
+                    output = DicomUIDGenerator.GenerateDerivedFromUUID().UID;
+                    return output as T;
+                }
+                case "SH":
+                case "AE":
+                case "CS":
+                case "PN":
+                case "ST":
+                case "UT":
+                {
+                    output = "no Value";
+                    break;
+                }
+            }
+            return output as T;
+        }
+
+        static (ushort group, ushort element) ParseDicomTagStringToTwoShorts(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));
+        }
+
     }
 }
diff --git a/src/InformaticsGateway/ExecutionPlugins/ExternalAppIncoming.cs b/src/InformaticsGateway/ExecutionPlugins/ExternalAppIncoming.cs
diff --git a/src/InformaticsGateway/ExecutionPlugins/ExternalAppOutgoing.cs b/src/InformaticsGateway/ExecutionPlugins/ExternalAppOutgoing.cs
diff --git a/src/InformaticsGateway/Logging/Log.5000.DataPlugins.cs b/src/InformaticsGateway/Logging/Log.5000.DataPlugins.cs
diff --git a/src/InformaticsGateway/Test/Services/Common/ExternalAppPluginTest.cs b/src/InformaticsGateway/Test/Services/Common/ExternalAppPluginTest.cs

Original file line number	Diff line number	Diff line change
`@@ -35,5 +35,12 @@ public class RemoteAppExecution`
`35`	`35`	`public List<string> Files { get; set; } = new();`
`36`	`36`	`public FileExportStatus Status { get; set; }`
`37`	`37`	`public Dictionary<string, string> OriginalValues { get; set; } = new();`
	`38`	`+ public Dictionary<string, string> ProxyValues { get; set; } = new();`
	`39`	`+ }`
	`40`	`+ public class RemoteAppExecutionTest`
	`41`	`+ {`
	`42`	`+ [JsonPropertyName("_id")]`
	`43`	`+ public string Id { get; set; } = default!;`
	`44`	`+ public DateTime RequestTime { get; set; } = DateTime.UtcNow;`
`38`	`45`	`}`
`39`	`46`	`}`
Original file line number	Diff line number	Diff line change
`@@ -40,6 +40,7 @@ public InformaticsGatewayContext(DbContextOptions<InformaticsGatewayContext> opt`
`40`	`40`	`public virtual DbSet<Payload> Payloads { get; set; }`
`41`	`41`	`public virtual DbSet<StorageMetadataWrapper> StorageMetadataWrapperEntities { get; set; }`
`42`	`42`	`public virtual DbSet<DicomAssociationInfo> DicomAssociationHistories { get; set; }`
	`43`	`+ public virtual DbSet<RemoteAppExecution> RemoteAppExecutions { get; set; }`
`43`	`44`
`44`	`45`	`protected override void OnModelCreating(ModelBuilder modelBuilder)`
`45`	`46`	`{`
`@@ -52,6 +53,7 @@ protected override void OnModelCreating(ModelBuilder modelBuilder)`
`52`	`53`	`modelBuilder.ApplyConfiguration(new PayloadConfiguration());`
`53`	`54`	`modelBuilder.ApplyConfiguration(new StorageMetadataWrapperEntityConfiguration());`
`54`	`55`	`modelBuilder.ApplyConfiguration(new DicomAssociationInfoConfiguration());`
	`56`	`+ modelBuilder.ApplyConfiguration(new RemoteAppExecutionConfiguration());`
`55`	`57`	`}`
`56`	`58`
`57`	`59`	`protected override void OnConfiguring(DbContextOptionsBuilder optionsBuilder)`
Original file line number	Diff line number	Diff line change
`@@ -31,7 +31,7 @@ namespace Monai.Deploy.InformaticsGateway.Database.EntityFramework.Repositories`
`31`	`31`	`{`
`32`	`32`	`public class RemoteAppExecutionRepository : IRemoteAppExecutionRepository, IDisposable`
`33`	`33`	`{`
`34`		`- private readonly ILogger<PayloadRepository> _logger;`
	`34`	`+ private readonly ILogger<RemoteAppExecutionRepository> _logger;`
`35`	`35`	`private readonly IServiceScope _scope;`
`36`	`36`	`private readonly InformaticsGatewayContext _informaticsGatewayContext;`
`37`	`37`	`private readonly AsyncRetryPolicy _retryPolicy;`
`@@ -44,7 +44,7 @@ public class RemoteAppExecutionRepository : IRemoteAppExecutionRepository, IDisp`
`44`	`44`
`45`	`45`	`public RemoteAppExecutionRepository(`
`46`	`46`	`IServiceScopeFactory serviceScopeFactory,`
`47`		`- ILogger<PayloadRepository> logger,`
	`47`	`+ ILogger<RemoteAppExecutionRepository> logger,`
`48`	`48`	`IOptions<InformaticsGatewayConfiguration> options)`
`49`	`49`	`{`
`50`	`50`	`Guard.Against.Null(serviceScopeFactory, nameof(serviceScopeFactory));`