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neildsouthneildsouth
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adding externalApp plugins
Signed-off-by: Neil South <[email protected]>
1 parent 8501ed7 commit 3b928d1

17 files changed

+780
-0
lines changed

‎src/Api/ExportRequestDataMessage.cs

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@@ -47,6 +47,11 @@ public string ExportTaskId
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get { return _exportRequest.ExportTaskId; }
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}
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public string WorkflowInstanceId
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{
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get { return _exportRequest.WorkflowInstanceId; }
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}
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public string CorrelationId
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{
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get { return _exportRequest.CorrelationId; }

‎src/Api/Storage/RemoteAppExecution.cs

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using System;
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using System.Collections.Generic;
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using FellowOakDicom;
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using Monai.Deploy.Messaging.Events;
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namespace Monai.Deploy.InformaticsGateway.Api.Storage
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{
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public class RemoteAppExecution
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{
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public DateTime RequestTime { get; set; } = DateTime.UtcNow;
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public string ExportTaskId { get; set; } = string.Empty;
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public string WorkflowInstanceId { get; set; } = string.Empty;
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public string CorrelationId { get; set; } = string.Empty;
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public string? StudyUid { get; set; }
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public string? OutgoingStudyUid { get; set; }
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public List<DestinationApplicationEntity> ExportDetails { get; set; } = new();
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public List<string> Files { get; set; } = new();
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public FileExportStatus Status { get; set; }
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public Dictionary<DicomTag, string> OriginalValues { get; set; } = new();
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}
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}

‎src/Client/Test/packages.lock.json

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‎src/Database/Api/Repositories/IRemoteAppExecutionRepository.cs

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using Monai.Deploy.InformaticsGateway.Api.Storage;
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namespace Monai.Deploy.InformaticsGateway.Database.Api.Repositories
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{
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public interface IRemoteAppExecutionRepository
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{
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Task<bool> AddAsync(RemoteAppExecution item, CancellationToken cancellationToken = default);
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Task<RemoteAppExecution?> GetAsync(string OutgoingStudyUid, CancellationToken cancellationToken = default);
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Task<int> RemoveAsync(string OutgoingStudyUid, CancellationToken cancellationToken = default);
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}
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}

‎src/Database/DatabaseManager.cs

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@@ -78,6 +78,7 @@ public static IServiceCollection ConfigureDatabase(this IServiceCollection servi
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services.AddScoped(typeof(IStorageMetadataRepository), typeof(EntityFramework.Repositories.StorageMetadataWrapperRepository));
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services.AddScoped(typeof(IPayloadRepository), typeof(EntityFramework.Repositories.PayloadRepository));
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services.AddScoped(typeof(IDicomAssociationInfoRepository), typeof(EntityFramework.Repositories.DicomAssociationInfoRepository));
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services.AddScoped(typeof(IRemoteAppExecutionRepository), typeof(EntityFramework.Repositories.RemoteAppExecutionRepository));
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return services;
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case DbType_MongoDb:
@@ -91,6 +92,7 @@ public static IServiceCollection ConfigureDatabase(this IServiceCollection servi
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services.AddScoped(typeof(IStorageMetadataRepository), typeof(MongoDB.Repositories.StorageMetadataWrapperRepository));
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services.AddScoped(typeof(IPayloadRepository), typeof(MongoDB.Repositories.PayloadRepository));
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services.AddScoped(typeof(IDicomAssociationInfoRepository), typeof(MongoDB.Repositories.DicomAssociationInfoRepository));
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services.AddScoped(typeof(IRemoteAppExecutionRepository), typeof(MongoDB.Repositories.RemoteAppExecutionRepository));
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return services;
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‎src/Database/EntityFramework/Repositories/RemoteAppExecutionRepository.cs

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/*
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* Copyright 2022 MONAI Consortium
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*
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* Licensed under the Apache License, Version 2.0 (the "License");
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* you may not use this file except in compliance with the License.
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* You may obtain a copy of the License at
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*
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* http://www.apache.org/licenses/LICENSE-2.0
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*
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* Unless required by applicable law or agreed to in writing, software
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* distributed under the License is distributed on an "AS IS" BASIS,
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* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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* See the License for the specific language governing permissions and
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* limitations under the License.
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*/
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using Ardalis.GuardClauses;
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using Microsoft.EntityFrameworkCore;
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using Microsoft.Extensions.DependencyInjection;
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using Microsoft.Extensions.Logging;
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using Microsoft.Extensions.Options;
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using Monai.Deploy.InformaticsGateway.Api.Storage;
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using Monai.Deploy.InformaticsGateway.Configuration;
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using Monai.Deploy.InformaticsGateway.Database.Api.Logging;
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using Monai.Deploy.InformaticsGateway.Database.Api.Repositories;
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using Polly;
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using Polly.Retry;
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namespace Monai.Deploy.InformaticsGateway.Database.EntityFramework.Repositories
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{
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public class RemoteAppExecutionRepository : IRemoteAppExecutionRepository, IDisposable
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{
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private readonly ILogger<PayloadRepository> _logger;
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private readonly IServiceScope _scope;
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private readonly InformaticsGatewayContext _informaticsGatewayContext;
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private readonly AsyncRetryPolicy _retryPolicy;
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private readonly DbSet<RemoteAppExecution> _dataset;
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private bool _disposedValue;
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public RemoteAppExecutionRepository(
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IServiceScopeFactory serviceScopeFactory,
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ILogger<PayloadRepository> logger,
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IOptions<InformaticsGatewayConfiguration> options)
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{
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Guard.Against.Null(serviceScopeFactory, nameof(serviceScopeFactory));
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Guard.Against.Null(options, nameof(options));
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_logger = logger ?? throw new ArgumentNullException(nameof(logger));
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_scope = serviceScopeFactory.CreateScope();
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_informaticsGatewayContext = _scope.ServiceProvider.GetRequiredService<InformaticsGatewayContext>();
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_retryPolicy = Policy.Handle<Exception>().WaitAndRetryAsync(
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options.Value.Database.Retries.RetryDelays,
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(exception, timespan, count, context) => _logger.DatabaseErrorRetry(timespan, count, exception));
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_dataset = _informaticsGatewayContext.Set<RemoteAppExecution>();
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}
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public async Task<bool> AddAsync(RemoteAppExecution item, CancellationToken cancellationToken = default)
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{
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Guard.Against.Null(item, nameof(item));
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return await _retryPolicy.ExecuteAsync(async () =>
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{
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var result = await _dataset.AddAsync(item, cancellationToken).ConfigureAwait(false);
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await _informaticsGatewayContext.SaveChangesAsync(cancellationToken).ConfigureAwait(false);
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return true;
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}).ConfigureAwait(false);
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}
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public async Task<int> RemoveAsync(string OriginalStudyUid, CancellationToken cancellationToken = default)
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{
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Guard.Against.Null(OriginalStudyUid, nameof(OriginalStudyUid));
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return await _retryPolicy.ExecuteAsync(async () =>
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{
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var result = await _dataset.SingleOrDefaultAsync(p => p.OutgoingStudyUid == OriginalStudyUid).ConfigureAwait(false);
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if (result is not null)
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{
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_dataset.Remove(result);
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await _informaticsGatewayContext.SaveChangesAsync(cancellationToken).ConfigureAwait(false);
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return 1;
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}
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return 0;
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}).ConfigureAwait(false);
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}
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public async Task<RemoteAppExecution?> GetAsync(string OutgoingStudyUid, CancellationToken cancellationToken = default)
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{
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Guard.Against.Null(OutgoingStudyUid, nameof(OutgoingStudyUid));
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return await _retryPolicy.ExecuteAsync(async () =>
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{
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var result = await _dataset.SingleOrDefaultAsync(p => p.OutgoingStudyUid == OutgoingStudyUid).ConfigureAwait(false);
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if (result is not null)
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{
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return result;
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}
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return default;
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}).ConfigureAwait(false);
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}
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protected virtual void Dispose(bool disposing)
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{
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if (!_disposedValue)
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{
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if (disposing)
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{
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_informaticsGatewayContext.Dispose();
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_scope.Dispose();
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}
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_disposedValue = true;
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}
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}
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public void Dispose()
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{
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// Do not change this code. Put cleanup code in 'Dispose(bool disposing)' method
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Dispose(disposing: true);
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GC.SuppressFinalize(this);
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}
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}
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}

‎src/Database/MongoDB/Repositories/RemoteAppExecutionRepository.cs

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using Ardalis.GuardClauses;
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using Microsoft.Extensions.DependencyInjection;
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using Microsoft.Extensions.Logging;
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using Microsoft.Extensions.Options;
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using Monai.Deploy.InformaticsGateway.Api.Storage;
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using Monai.Deploy.InformaticsGateway.Configuration;
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using Monai.Deploy.InformaticsGateway.Database.Api.Logging;
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using Monai.Deploy.InformaticsGateway.Database.Api.Repositories;
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using Monai.Deploy.InformaticsGateway.Database.MongoDB.Configurations;
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using MongoDB.Driver;
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using Polly;
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using Polly.Retry;
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namespace Monai.Deploy.InformaticsGateway.Database.MongoDB.Repositories
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{
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public class RemoteAppExecutionRepository : IRemoteAppExecutionRepository, IDisposable
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{
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private readonly ILogger<RemoteAppExecutionRepository> _logger;
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private readonly IServiceScope _scope;
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private readonly AsyncRetryPolicy _retryPolicy;
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private readonly IMongoCollection<RemoteAppExecution> _collection;
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private bool _disposedValue;
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public RemoteAppExecutionRepository(IServiceScopeFactory serviceScopeFactory,
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ILogger<RemoteAppExecutionRepository> logger,
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IOptions<InformaticsGatewayConfiguration> options,
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IOptions<MongoDBOptions> mongoDbOptions)
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{
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Guard.Against.Null(serviceScopeFactory, nameof(serviceScopeFactory));
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Guard.Against.Null(options, nameof(options));
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Guard.Against.Null(mongoDbOptions, nameof(mongoDbOptions));
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_logger = logger ?? throw new ArgumentNullException(nameof(logger));
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_scope = serviceScopeFactory.CreateScope();
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_retryPolicy = Policy.Handle<Exception>().WaitAndRetryAsync(
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options.Value.Database.Retries.RetryDelays,
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(exception, timespan, count, context) => _logger.DatabaseErrorRetry(timespan, count, exception));
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var mongoDbClient = _scope.ServiceProvider.GetRequiredService<IMongoClient>();
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var mongoDatabase = mongoDbClient.GetDatabase(mongoDbOptions.Value.DaatabaseName);
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_collection = mongoDatabase.GetCollection<RemoteAppExecution>(nameof(RemoteAppExecution));
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CreateIndexes();
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}
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private void CreateIndexes()
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{
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var options = new CreateIndexOptions { Unique = true, ExpireAfter = TimeSpan.FromDays(7), Name = "RequestTime" };
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var indexDefinitionState = Builders<RemoteAppExecution>.IndexKeys.Ascending(_ => _.OutgoingStudyUid);
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var indexModel = new CreateIndexModel<RemoteAppExecution>(indexDefinitionState, options);
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_collection.Indexes.CreateOne(indexModel);
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}
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public async Task<bool> AddAsync(RemoteAppExecution item, CancellationToken cancellationToken = default)
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{
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Guard.Against.Null(item, nameof(item));
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return await _retryPolicy.ExecuteAsync(async () =>
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{
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await _collection.InsertOneAsync(item, cancellationToken: cancellationToken).ConfigureAwait(false);
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return true;
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}).ConfigureAwait(false);
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}
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public async Task<int> RemoveAsync(string OutgoingStudyUid, CancellationToken cancellationToken = default)
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{
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return await _retryPolicy.ExecuteAsync(async () =>
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{
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var results = await _collection.DeleteManyAsync(Builders<RemoteAppExecution>.Filter.Where(p => p.OutgoingStudyUid == OutgoingStudyUid), cancellationToken).ConfigureAwait(false);
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return Convert.ToInt32(results.DeletedCount);
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}).ConfigureAwait(false);
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}
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public async Task<RemoteAppExecution?> GetAsync(string OutgoingStudyUid, CancellationToken cancellationToken = default)
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{
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return await _retryPolicy.ExecuteAsync(async () =>
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{
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return await _collection.Find(p => p.OutgoingStudyUid == OutgoingStudyUid).FirstOrDefaultAsync().ConfigureAwait(false);
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}).ConfigureAwait(false);
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}
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public void Dispose(bool disposing)
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{
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if (!_disposedValue)
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{
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if (disposing)
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{
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_scope.Dispose();
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}
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_disposedValue = true;
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}
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}
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public void Dispose()
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{
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// Do not change this code. Put cleanup code in 'Dispose(bool disposing)' method
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Dispose(disposing: true);
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GC.SuppressFinalize(this);
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}
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}
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}

‎src/InformaticsGateway/ExecutionPlugins/ExternalAppIncoming.cs

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using System;
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using System.Threading.Tasks;
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using FellowOakDicom;
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using Microsoft.Extensions.DependencyInjection;
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using Microsoft.Extensions.Logging;
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using Monai.Deploy.InformaticsGateway.Api;
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using Monai.Deploy.InformaticsGateway.Api.Storage;
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using Monai.Deploy.InformaticsGateway.Database.Api.Repositories;
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namespace Monai.Deploy.InformaticsGateway.ExecutionPlugins
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{
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public class ExternalAppIncoming : IInputDataPlugin
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{
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private readonly ILogger<ExternalAppIncoming> _logger;
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private readonly IServiceScopeFactory _serviceScopeFactory;
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public ExternalAppIncoming(
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ILogger<ExternalAppIncoming> logger,
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IServiceScopeFactory serviceScopeFactory)
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{
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_logger = logger ?? throw new ArgumentNullException(nameof(logger));
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_serviceScopeFactory = serviceScopeFactory ?? throw new ArgumentNullException(nameof(serviceScopeFactory));
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}
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public async Task<(DicomFile dicomFile, FileStorageMetadata fileMetadata)> Execute(DicomFile dicomFile, FileStorageMetadata fileMetadata)
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{
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var scope = _serviceScopeFactory.CreateScope();
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var repository = scope.ServiceProvider.GetRequiredService<IRemoteAppExecutionRepository>();
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var incommingStudyUid = dicomFile.Dataset.GetString(DicomTag.StudyInstanceUID);
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var remoteAppExecution = await repository.GetAsync(incommingStudyUid);
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if (remoteAppExecution is null)
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{
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_logger.LogOriginalStudyUidNotFound(incommingStudyUid);
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return (dicomFile, fileMetadata);
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}
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foreach (var key in remoteAppExecution.OriginalValues.Keys)
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{
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dicomFile.Dataset.AddOrUpdate(key, remoteAppExecution.OriginalValues[key]);
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}
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dicomFile.Dataset.AddOrUpdate(DicomTag.StudyInstanceUID, remoteAppExecution.StudyUid);
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fileMetadata.WorkflowInstanceId = remoteAppExecution.WorkflowInstanceId;
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fileMetadata.TaskId = remoteAppExecution.ExportTaskId;
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return (dicomFile, fileMetadata);
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}
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}
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}

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