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Refactor integration tests
Signed-off-by: Victor Chang <[email protected]>
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‎tests/Integration.Test/Common/Assertions.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 System.Globalization;
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using System.Text;
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using System.Text.Json;
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using System.Text.Json.Nodes;
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using System.Xml;
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using Ardalis.GuardClauses;
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using FellowOakDicom;
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using FellowOakDicom.Serialization;
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using Minio;
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using Monai.Deploy.InformaticsGateway.Configuration;
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using Monai.Deploy.InformaticsGateway.Integration.Test.Drivers;
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using Monai.Deploy.InformaticsGateway.Integration.Test.Hooks;
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using Monai.Deploy.Messaging.Events;
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using Monai.Deploy.Messaging.Messages;
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using TechTalk.SpecFlow.Infrastructure;
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namespace Monai.Deploy.InformaticsGateway.Integration.Test.Common
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{
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internal class Assertions
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{
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private readonly Configurations _configurations;
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private readonly InformaticsGatewayConfiguration _options;
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private readonly ISpecFlowOutputHelper _outputHelper;
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public Assertions(Configurations configurations, InformaticsGatewayConfiguration options, ISpecFlowOutputHelper outputHelper)
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{
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_configurations = configurations ?? throw new ArgumentNullException(nameof(configurations));
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_options = options ?? throw new ArgumentNullException(nameof(options));
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_outputHelper = outputHelper ?? throw new ArgumentNullException(nameof(outputHelper));
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}
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internal async Task ShouldHaveUploadedDicomDataToMinio(IReadOnlyList<Message> messages, Dictionary<string, string> fileHashes)
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{
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Guard.Against.Null(messages);
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Guard.Against.NullOrEmpty(fileHashes);
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var minioClient = GetMinioClient();
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foreach (var message in messages)
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{
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var request = message.ConvertTo<WorkflowRequestEvent>();
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foreach (var file in request.Payload)
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{
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var dicomValidationKey = string.Empty;
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var getObjectArgs = new GetObjectArgs()
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.WithBucket(request.Bucket)
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.WithObject($"{request.PayloadId}/{file.Path}")
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.WithCallbackStream((stream) =>
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{
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using var memoryStream = new MemoryStream();
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stream.CopyTo(memoryStream);
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memoryStream.Position = 0;
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var dicomFile = DicomFile.Open(memoryStream);
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dicomValidationKey = dicomFile.GenerateFileName();
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fileHashes.Should().ContainKey(dicomValidationKey).WhoseValue.Should().Be(dicomFile.CalculateHash());
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});
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await minioClient.GetObjectAsync(getObjectArgs);
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var getMetadataObjectArgs = new GetObjectArgs()
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.WithBucket(request.Bucket)
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.WithObject($"{request.PayloadId}/{file.Metadata}")
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.WithCallbackStream((stream) =>
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{
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using var memoryStream = new MemoryStream();
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stream.CopyTo(memoryStream);
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var json = Encoding.UTF8.GetString(memoryStream.ToArray());
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var dicomFileFromJson = DicomJson.ConvertJsonToDicom(json);
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var key = dicomFileFromJson.GenerateFileName();
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key.Should().Be(dicomValidationKey);
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});
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await minioClient.GetObjectAsync(getMetadataObjectArgs);
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}
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}
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}
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internal async Task ShouldHaveUploadedFhirDataToMinio(IReadOnlyList<Message> messages, Dictionary<string, string> fhirData)
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{
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Guard.Against.Null(messages);
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var minioClient = GetMinioClient();
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foreach (var message in messages)
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{
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message.ApplicationId.Should().Be(MessageBrokerConfiguration.InformaticsGatewayApplicationId);
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var request = message.ConvertTo<WorkflowRequestEvent>();
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request.Should().NotBeNull();
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request.FileCount.Should().Be(1);
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foreach (var file in request.Payload)
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{
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var getObjectArgs = new GetObjectArgs()
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.WithBucket(request.Bucket)
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.WithObject($"{request.PayloadId}/{file.Path}")
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.WithCallbackStream((stream) =>
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{
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using var memoryStream = new MemoryStream();
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stream.CopyTo(memoryStream);
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memoryStream.Position = 0;
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var data = Encoding.UTF8.GetString(memoryStream.ToArray());
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data.Should().NotBeNullOrWhiteSpace();
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var incomingFilename = Path.GetFileName(file.Path);
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var storedFileKey = fhirData.Keys.FirstOrDefault(p => p.EndsWith(incomingFilename));
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storedFileKey.Should().NotBeNull();
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_outputHelper.WriteLine($"Validating file {storedFileKey}...");
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if (incomingFilename.EndsWith(".json", true, CultureInfo.InvariantCulture))
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{
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ValidateJson(fhirData[storedFileKey], data);
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}
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else
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{
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ValidateXml(fhirData[storedFileKey], data);
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}
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});
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await minioClient.GetObjectAsync(getObjectArgs);
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}
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}
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}
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internal async Task ShouldHaveUploadedHl7ataToMinio(IReadOnlyList<Message> messages)
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{
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Guard.Against.Null(messages);
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var minioClient = GetMinioClient();
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foreach (var message in messages)
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{
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var request = message.ConvertTo<WorkflowRequestEvent>();
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var listOjbectsArgs = new ListObjectsArgs()
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.WithBucket(request.Bucket)
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.WithPrefix(request.PayloadId.ToString())
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.WithRecursive(true);
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var results = minioClient.ListObjectsAsync(listOjbectsArgs);
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results.Subscribe(item =>
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{
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_outputHelper.WriteLine($"File => {item.Key}...");
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},
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exception =>
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{
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_outputHelper.WriteLine($"Error listing files {exception.Message}");
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});
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foreach (var file in request.Payload)
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{
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_outputHelper.WriteLine($"Verifying file => {request.PayloadId}/{file.Path}...");
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var getObjectArgs = new GetObjectArgs()
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.WithBucket(request.Bucket)
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.WithObject($"{request.PayloadId}/{file.Path}")
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.WithCallbackStream((stream) =>
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{
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using var memoryStream = new MemoryStream();
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stream.CopyTo(memoryStream);
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memoryStream.Position = 0;
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var data = Encoding.UTF8.GetString(memoryStream.ToArray());
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var hl7Message = new HL7.Dotnetcore.Message(data);
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hl7Message.ParseMessage().Should().BeTrue();
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});
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await minioClient.GetObjectAsync(getObjectArgs);
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}
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}
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}
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internal void ShouldHaveCorrectNumberOfWorkflowRequestMessages(DataProvider dataProvider, IReadOnlyList<Message> messages, int count)
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{
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Guard.Against.Null(dataProvider);
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Guard.Against.Null(messages);
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messages.Should().NotBeNullOrEmpty().And.HaveCount(count);
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foreach (var message in messages)
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{
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message.ApplicationId.Should().Be(MessageBrokerConfiguration.InformaticsGatewayApplicationId);
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var request = message.ConvertTo<WorkflowRequestEvent>();
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request.Should().NotBeNull();
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request.FileCount.Should().Be((dataProvider.DicomSpecs.NumberOfExpectedFiles(dataProvider.StudyGrouping)));
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if (dataProvider.Workflows is not null)
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{
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request.Workflows.Should().Equal(dataProvider.Workflows);
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}
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}
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}
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internal void ShouldHaveCorrectNumberOfWorkflowRequestMessagesAndAcrRequest(DataProvider dataProvider, IReadOnlyList<Message> messages, int count)
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{
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Guard.Against.Null(dataProvider);
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Guard.Against.Null(messages);
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messages.Should().NotBeNullOrEmpty().And.HaveCount(count);
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foreach (var message in messages)
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{
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message.ApplicationId.Should().Be(MessageBrokerConfiguration.InformaticsGatewayApplicationId);
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var request = message.ConvertTo<WorkflowRequestEvent>();
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request.Should().NotBeNull();
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request.FileCount.Should().Be(dataProvider.DicomSpecs.FileCount);
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request.Workflows.Should().Equal(dataProvider.AcrRequest.Application.Id);
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}
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}
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internal void ShouldHaveCorrectNumberOfWorkflowRequestMessagesAndHl7Messages(Hl7Messages hL7Specs, IReadOnlyList<Message> messages, int count)
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{
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Guard.Against.Null(hL7Specs);
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Guard.Against.Null(messages);
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messages.Should().NotBeNullOrEmpty().And.HaveCount(count);
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foreach (var message in messages)
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{
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message.ApplicationId.Should().Be(MessageBrokerConfiguration.InformaticsGatewayApplicationId);
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var request = message.ConvertTo<WorkflowRequestEvent>();
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request.Should().NotBeNull();
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request.FileCount.Should().Be(hL7Specs.Files.Count);
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}
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}
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private MinioClient GetMinioClient() => new MinioClient()
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.WithEndpoint(_options.Storage.Settings["endpoint"])
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.WithCredentials(_options.Storage.Settings["accessKey"], _options.Storage.Settings["accessToken"])
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.Build();
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private void ValidateXml(string expected, string actual)
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{
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expected = FormatXml(expected);
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expected.Should().Be(actual);
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}
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private string FormatXml(string xml)
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{
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var xmlDocument = new XmlDocument();
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xmlDocument.LoadXml(xml);
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var sb = new StringBuilder();
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using (var xmlWriter = XmlWriter.Create(sb, new XmlWriterSettings { Encoding = Encoding.UTF8, Indent = true }))
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{
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xmlDocument.Save(xmlWriter);
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}
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return sb.ToString();
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}
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private void ValidateJson(string expected, string actual)
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{
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expected = FormatJson(expected);
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expected.Should().Be(actual);
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}
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private string FormatJson(string expected)
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{
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var jsonDoc = JsonNode.Parse(expected);
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return jsonDoc.ToJsonString(new JsonSerializerOptions { WriteIndented = true });
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}
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internal void ShoulddHaveCorrectNumberOfAckMessages(Dictionary<string, string> responses)
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{
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foreach (var file in responses.Keys)
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{
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_outputHelper.WriteLine($"Verifying acknowledgement for {file}...");
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var message = new HL7.Dotnetcore.Message(responses[file]);
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message.ParseMessage();
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var segment = message.DefaultSegment("MSH");
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_outputHelper.WriteLine($"ACK Value= {segment.Value}...");
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segment.Fields(9).Value.Should().Be("ACK");
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}
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}
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}
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}

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