change around config and fixs for plugins

Signed-off-by: Neil South <[email protected]>

Author: neildsouth

.github/workflows/package-cleanup.yml

@@ -17,8 +17,8 @@
 name: Cleanup Pre-release Packages
 
 on:
-  schedule:
-  - cron: "0 0 * * *"
+  # schedule:
+  # - cron: "0 0 * * *"
   workflow_dispatch:
 
 jobs:

Dockerfile

@@ -12,7 +12,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-FROM mcr.microsoft.com/dotnet/sdk:6.0-jammy as build
+FROM mcr.microsoft.com/dotnet/sdk:6.0-focal as build
 
 # Install the tools
 RUN dotnet tool install --tool-path /tools dotnet-trace
@@ -26,7 +26,7 @@ RUN echo "Building MONAI Deploy Informatics Gateway..."
 RUN dotnet publish -c Release -o out --nologo src/InformaticsGateway/Monai.Deploy.InformaticsGateway.csproj
 
 # Build runtime image
-FROM mcr.microsoft.com/dotnet/aspnet:6.0-jammy
+FROM mcr.microsoft.com/dotnet/aspnet:6.0-focal
 
 # Enable elastic client compatibility mode
 ENV ELASTIC_CLIENT_APIVERSIONING=true

docs/api/rest/dicom-association.md

@@ -0,0 +1,59 @@
+<!--
+  ~ Copyright 2021-2023 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.
+-->
+
+# DICOM Association information
+
+The `/dicom-associations' endpoint is for retrieving a list of information regarding dicom
+associations.
+
+## GET /dicom-associations/
+
+#### Query Parameters
+
+| Name       | Type     | Description                                 |
+|------------|----------|---------------------------------------------|
+| startTime  | DateTime | (Optional) Start date to query from.        |
+| endTime    | DateTime | (Optional) End date to query from.          |
+| pageNumber | Number   | (Optional) Page number to query.(default 0) |
+| pageSize   | Number   | (Optional) Page size of query.              |
+
+Max & Defaults for PageSize can be set in appSettings.
+
+```json
+"endpointSettings": {
+  "defaultPageSize": number,
+  "maxPageSize": number
+}
+```
+
+Endpoint returns a paged result for example
+
+```json
+{
+  "PageNumber": 1,
+  "PageSize": 10,
+  "FirstPage": "/payload?pageNumber=1&pageSize=10",
+  "LastPage": "/payload?pageNumber=1&pageSize=10",
+  "TotalPages": 1,
+  "TotalRecords": 3,
+  "NextPage": null,
+  "PreviousPage": null,
+  "Data": [...]
+  "Succeeded": true,
+  "Errors": null,
+  "Message": null
+}
+```

src/Client/Test/packages.lock.json

@@ -1921,6 +1921,7 @@
           "Microsoft.Extensions.Configuration": "[6.0.1, )",
           "Microsoft.Extensions.Configuration.FileExtensions": "[6.0.0, )",
           "Microsoft.Extensions.Configuration.Json": "[6.0.0, )",
+          "Microsoft.Extensions.Options.ConfigurationExtensions": "[6.0.0, )",
           "Monai.Deploy.InformaticsGateway.Api": "[0.4.1, )",
           "Monai.Deploy.InformaticsGateway.Configuration": "[1.0.0, )",
           "Monai.Deploy.InformaticsGateway.Database.Api": "[1.0.0, )",

src/Configuration/DatabaseConfiguration.cs renamed to src/Configuration/HttpEndpointSettings.cs

@@ -1,5 +1,6 @@
 /*
- * Copyright 2021-2022 MONAI Consortium
+ * Copyright 2021-2023 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.
@@ -18,12 +19,12 @@
 
 namespace Monai.Deploy.InformaticsGateway.Configuration
 {
-    public class DatabaseConfiguration
+    public class HttpEndpointSettings
     {
-        /// <summary>
-        /// Gets or sets retry options relate to reading/writing to the database.
-        /// </summary>
-        [ConfigurationKeyName("retries")]
-        public RetryConfiguration Retries { get; set; } = new RetryConfiguration();
+        [ConfigurationKeyName("defaultPageSize")]
+        public int DefaultPageSize { get; set; } = 10;
+
+        [ConfigurationKeyName("maxPageSize")]
+        public int MaxPageSize { get; set; } = 10;
     }
 }

src/Configuration/InformaticsGatewayConfiguration.cs

@@ -70,18 +70,6 @@ public class InformaticsGatewayConfiguration
         [ConfigurationKeyName("messaging")]
         public MessageBrokerConfiguration Messaging { get; set; }
 
-        /// <summary>
-        /// Represents the <c>database</c> section of the configuration file.
-        /// </summary>
-        [ConfigurationKeyName("database")]
-        public DatabaseConfiguration Database { get; set; }
-
-        /// <summary>
-        /// Represents the <c>pluginConfiguration</c> section of the configuration file.
-        /// </summary>
-        [ConfigurationKeyName("plugins")]
-        public PlugInConfiguration PlugInConfigurations { get; set; }
-
         public InformaticsGatewayConfiguration()
         {
             Dicom = new DicomConfiguration();
@@ -90,9 +78,7 @@ public InformaticsGatewayConfiguration()
             Fhir = new FhirConfiguration();
             Export = new DataExportConfiguration();
             Messaging = new MessageBrokerConfiguration();
-            Database = new DatabaseConfiguration();
             Hl7 = new Hl7Configuration();
-            PlugInConfigurations = new PlugInConfiguration();
         }
     }
 }

src/Configuration/RetryConfiguration.cs

@@ -29,7 +29,7 @@ public class RetryConfiguration
         /// Default is 250, 500, 1000.
         /// </summary>
         [ConfigurationKeyName("delays")]
-        public int[] DelaysMilliseconds { get; set; } = new[] { 750, 1200, 2500 };
+        public int[] DelaysMilliseconds { get; set; }
 
         // Gets the delays in TimeSpan objects
         public IEnumerable<TimeSpan> RetryDelays
@@ -42,5 +42,12 @@ public IEnumerable<TimeSpan> RetryDelays
                 }
             }
         }
+        public RetryConfiguration()
+        {
+            if (DelaysMilliseconds is null || DelaysMilliseconds.Length == 0)
+            {
+                DelaysMilliseconds = new[] { 250, 500, 1000 };
+            }
+        }
     }
 }

src/Database/Api/DatabaseOptions.cs

@@ -15,12 +15,19 @@
  */
 
 using Microsoft.Extensions.Configuration;
+using Monai.Deploy.InformaticsGateway.Configuration;
 
 namespace Monai.Deploy.InformaticsGateway.Database.Api
 {
     public class DatabaseOptions
     {
         [ConfigurationKeyName("DatabaseName")]
         public string DatabaseName { get; set; } = string.Empty;
+
+        /// <summary>
+        /// Gets or sets retry options relate to reading/writing to the database.
+        /// </summary>
+        [ConfigurationKeyName("retries")]
+        public RetryConfiguration Retries { get; set; } = new RetryConfiguration();
     }
 }

src/Database/Api/DatabaseRegistrationBase.cs

@@ -14,13 +14,14 @@
  * limitations under the License.
  */
 
+using Microsoft.Extensions.Configuration;
 using Microsoft.Extensions.DependencyInjection;
 using Microsoft.Extensions.Logging;
 
 namespace Monai.Deploy.InformaticsGateway.Database.Api
 {
     public abstract class DatabaseRegistrationBase
     {
-        public abstract IServiceCollection Configure(IServiceCollection services, DatabaseType databaseType, string? connectionString, ILogger logger);
+        public abstract IServiceCollection Configure(IServiceCollection services, DatabaseType databaseType, IConfigurationSection? connectionstringConfigurationSection, IConfigurationSection? pluginsConfigurationSection, ILoggerFactory loggerFactory);
     }
 }

src/Database/Api/Repositories/IDicomAssociationInfoRepository.cs

@@ -23,5 +23,20 @@ public interface IDicomAssociationInfoRepository
         Task<List<DicomAssociationInfo>> ToListAsync(CancellationToken cancellationToken = default);
 
         Task<DicomAssociationInfo> AddAsync(DicomAssociationInfo item, CancellationToken cancellationToken = default);
+
+        /// <summary>
+        /// Retrieves a list of DicomAssociationInfo in the database.
+        /// </summary>
+        Task<IList<DicomAssociationInfo>> GetAllAsync(int skip,
+            int? limit,
+            DateTime startTime,
+            DateTime endTime,
+            CancellationToken cancellationToken);
+
+        /// <summary>
+        /// Gets count of objects
+        /// </summary>
+        /// <returns>Count of objects.</returns>
+        Task<long> CountAsync();
     }
 }

src/Database/Api/Repositories/InferenceRequestRepositoryBase.cs

@@ -19,19 +19,18 @@
 using Microsoft.Extensions.Options;
 using Monai.Deploy.InformaticsGateway.Api;
 using Monai.Deploy.InformaticsGateway.Api.Rest;
-using Monai.Deploy.InformaticsGateway.Configuration;
 using Monai.Deploy.InformaticsGateway.Database.Api.Logging;
 
 namespace Monai.Deploy.InformaticsGateway.Database.Api.Repositories
 {
     public abstract class InferenceRequestRepositoryBase : IInferenceRequestRepository
     {
         private readonly ILogger _logger;
-        private readonly IOptions<InformaticsGatewayConfiguration> _options;
+        private readonly IOptions<DatabaseOptions> _options;
 
         protected InferenceRequestRepositoryBase(
             ILogger logger,
-            IOptions<InformaticsGatewayConfiguration> options)
+            IOptions<DatabaseOptions> options)
         {
             _logger = logger ?? throw new ArgumentNullException(nameof(logger));
             _options = options ?? throw new ArgumentNullException(nameof(options));
@@ -72,7 +71,7 @@ public async Task UpdateAsync(InferenceRequest inferenceRequest, InferenceReques
             }
             else
             {
-                if (++inferenceRequest.TryCount > _options.Value.Database.Retries.DelaysMilliseconds.Length)
+                if (++inferenceRequest.TryCount > _options.Value.Retries.DelaysMilliseconds.Length)
                 {
                     _logger.InferenceRequestUpdateExceededMaximumRetries();
                     inferenceRequest.State = InferenceRequestState.Completed;

src/Database/Api/StorageMetadataWrapper.cs

@@ -27,7 +27,7 @@ namespace Monai.Deploy.InformaticsGateway.Database.Api
     /// </summary>
     public class StorageMetadataWrapper : MongoDBEntityBase
     {
-        private readonly JsonSerializerOptions _options;
+        //private readonly JsonSerializerOptions _options;
 
         [JsonPropertyName("correlationId")]
         public string CorrelationId { get; set; } = string.Empty;
@@ -92,4 +92,4 @@ public override string ToString()
             return $"Identity: {Identity}";
         }
     }
-}
+}

src/Database/DatabaseManager.cs

@@ -63,16 +63,18 @@ public static IHealthChecksBuilder AddDatabaseHealthCheck(this IHealthChecksBuil
             }
         }
 
-        public static IServiceCollection ConfigureDatabase(this IServiceCollection services, IConfigurationSection? connectionStringConfigurationSection, ILogger logger)
-            => services.ConfigureDatabase(connectionStringConfigurationSection, new FileSystem(), logger);
+        public static IServiceCollection ConfigureDatabase(this IServiceCollection services, IConfigurationSection? connectionStringConfigurationSection, IConfigurationSection? pluginsConfigurationSection, ILoggerFactory loggerFactory)
+            => services.ConfigureDatabase(connectionStringConfigurationSection, pluginsConfigurationSection, new FileSystem(), loggerFactory);
 
-        public static IServiceCollection ConfigureDatabase(this IServiceCollection services, IConfigurationSection? connectionStringConfigurationSection, IFileSystem fileSystem, ILogger logger)
+        public static IServiceCollection ConfigureDatabase(this IServiceCollection services, IConfigurationSection? connectionStringConfigurationSection, IConfigurationSection? pluginsConfigurationSection, IFileSystem fileSystem, ILoggerFactory loggerFactory)
         {
+            var logger = loggerFactory.CreateLogger("DatabaseManager");
+
             if (connectionStringConfigurationSection is null)
             {
                 throw new ConfigurationException("No database connections found in configuration section 'ConnectionStrings'.");
             }
-
+            services.Configure<DatabaseOptions>(connectionStringConfigurationSection.GetSection("DatabaseOptions"));
             var databaseType = connectionStringConfigurationSection["Type"].ToLowerInvariant();
             switch (databaseType)
             {
@@ -90,13 +92,12 @@ public static IServiceCollection ConfigureDatabase(this IServiceCollection servi
                     services.AddScoped(typeof(IDicomAssociationInfoRepository), typeof(EntityFramework.Repositories.DicomAssociationInfoRepository));
                     services.AddScoped(typeof(IVirtualApplicationEntityRepository), typeof(EntityFramework.Repositories.VirtualApplicationEntityRepository));
 
-                    services.ConfigureDatabaseFromPlugIns(DatabaseType.EntityFramework, fileSystem, connectionStringConfigurationSection, logger);
+                    services.ConfigureDatabaseFromPlugIns(DatabaseType.EntityFramework, fileSystem, connectionStringConfigurationSection, pluginsConfigurationSection, loggerFactory);
                     return services;
 
                 case DbType_MongoDb:
+                    var terst = connectionStringConfigurationSection[SR.DatabaseConnectionStringKey];
                     services.AddSingleton<IMongoClient, MongoClient>(s => new MongoClient(connectionStringConfigurationSection[SR.DatabaseConnectionStringKey]));
-                    services.Configure<DatabaseOptions>(connectionStringConfigurationSection);
-
                     services.AddScoped<IDatabaseMigrationManager, MongoDatabaseMigrationManager>();
                     services.AddScoped(typeof(IDestinationApplicationEntityRepository), typeof(MongoDB.Repositories.DestinationApplicationEntityRepository));
                     services.AddScoped(typeof(IInferenceRequestRepository), typeof(MongoDB.Repositories.InferenceRequestRepository));
@@ -107,7 +108,7 @@ public static IServiceCollection ConfigureDatabase(this IServiceCollection servi
                     services.AddScoped(typeof(IDicomAssociationInfoRepository), typeof(MongoDB.Repositories.DicomAssociationInfoRepository));
                     services.AddScoped(typeof(IVirtualApplicationEntityRepository), typeof(MongoDB.Repositories.VirtualApplicationEntityRepository));
 
-                    services.ConfigureDatabaseFromPlugIns(DatabaseType.MongoDb, fileSystem, connectionStringConfigurationSection, logger);
+                    services.ConfigureDatabaseFromPlugIns(DatabaseType.MongoDb, fileSystem, connectionStringConfigurationSection, pluginsConfigurationSection, loggerFactory);
 
                     return services;
 
@@ -120,7 +121,8 @@ public static IServiceCollection ConfigureDatabaseFromPlugIns(this IServiceColle
             DatabaseType databaseType,
             IFileSystem fileSystem,
             IConfigurationSection? connectionStringConfigurationSection,
-            ILogger logger)
+            IConfigurationSection? pluginsConfigurationSection,
+            ILoggerFactory loggerFactory)
         {
             Guard.Against.Null(fileSystem, nameof(fileSystem));
 
@@ -133,7 +135,7 @@ public static IServiceCollection ConfigureDatabaseFromPlugIns(this IServiceColle
                 {
                     throw new ConfigurationException($"Error activating database registration from type '{type.FullName}'.");
                 }
-                registrar.Configure(services, databaseType, connectionStringConfigurationSection?[SR.DatabaseConnectionStringKey], logger);
+                registrar.Configure(services, databaseType, connectionStringConfigurationSection, pluginsConfigurationSection, loggerFactory);
             }
             return services;
         }
@@ -167,8 +169,7 @@ internal static Assembly[] LoadAssemblyFromPlugInsDirectory(IFileSystem fileSyst
 
             foreach (var plugin in plugins)
             {
-                var asesmblyeData = fileSystem.File.ReadAllBytes(plugin);
-                assemblies.Add(Assembly.Load(asesmblyeData));
+                assemblies.Add(Assembly.LoadFrom(plugin));
             }
             return assemblies.ToArray();
         }

src/Database/EntityFramework/Configuration/DicomAssociationInfoConfiguration.cs

@@ -29,7 +29,7 @@ internal class DicomAssociationInfoConfiguration : IEntityTypeConfiguration<Dico
         public void Configure(EntityTypeBuilder<DicomAssociationInfo> builder)
         {
             var comparer = new ValueComparer<HashSet<string>>(
-                (c1, c2) => c1.SequenceEqual(c2),
+                (c1, c2) => c1!.SequenceEqual(c2!),
                 c => c.Aggregate(0, (a, v) => HashCode.Combine(a, v.GetHashCode())),
                 c => c.ToHashSet());
 
@@ -50,7 +50,7 @@ public void Configure(EntityTypeBuilder<DicomAssociationInfo> builder)
             builder.Property(j => j.PayloadIds).IsRequired()
                 .HasConversion(
                         v => JsonSerializer.Serialize(v, jsonSerializerSettings),
-                        v => JsonSerializer.Deserialize<HashSet<string>>(v, jsonSerializerSettings))
+                        v => JsonSerializer.Deserialize<HashSet<string>>(v, jsonSerializerSettings) ?? new HashSet<string>())
                 .Metadata.SetValueComparer(comparer);
         }
     }