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gh-41 Add DICOM Export test feature
Signed-off-by: Victor Chang <[email protected]>
1 parent 234cf3f commit 731b058

24 files changed

+866
-194
lines changed

‎.github/workflows/ci.yml

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@@ -276,6 +276,7 @@ jobs:
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tests/Integration.Test/LivingDoc.html
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tests/Integration.Test/metrics.log
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tests/Integration.Test/services.log
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tests/Integration.Test/run.log
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retention-days: 30
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‎.vscode/launch.json

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@@ -21,7 +21,7 @@
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"request": "launch",
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"preLaunchTask": "build",
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// If you have changed target frameworks, make sure to update the program path.
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"program": "${workspaceFolder}/src/InformaticsGateway/bin/Debug/net5.0/Monai.Deploy.InformaticsGateway",
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"program": "${workspaceFolder}/src/InformaticsGateway/bin/Debug/net6.0/Monai.Deploy.InformaticsGateway",
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"args": [],
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"cwd": "${workspaceFolder}/src/InformaticsGateway",
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// For more information about the 'console' field, see https://aka.ms/VSCode-CS-LaunchJson-Console
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"request": "attach"
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}
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]
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}
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}

‎src/DicomWebClient/Monai.Deploy.InformaticsGateway.DicomWeb.Client.csproj

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@@ -1,15 +1,15 @@
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<!--
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// Copyright 2021 MONAI Consortium
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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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// http://www.apache.org/licenses/LICENSE-2.0
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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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Copyright 2021 MONAI Consortium
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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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http://www.apache.org/licenses/LICENSE-2.0
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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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<Project Sdk="Microsoft.NET.Sdk">
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@@ -35,9 +35,9 @@
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<ItemGroup>
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<PackageReference Include="Ardalis.GuardClauses" Version="3.3.0" />
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<PackageReference Include="fo-dicom" Version="5.0.1" />
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<PackageReference Include="GitVersion.MsBuild" Version="5.8.1">
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<PrivateAssets>All</PrivateAssets>
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</PackageReference>
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<PackageReference Include="GitVersion.MsBuild" Version="5.8.1">
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<PrivateAssets>All</PrivateAssets>
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</PackageReference>
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<PackageReference Include="Microsoft.AspNet.WebApi.Client" Version="5.2.7" />
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<PackageReference Include="Microsoft.Net.Http.Headers" Version="2.2.8" />
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<PackageReference Include="Microsoft.Extensions.Http" Version="6.0.0" />
@@ -48,4 +48,4 @@
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<ProjectReference Include="..\Client.Common\Monai.Deploy.InformaticsGateway.Client.Common.csproj" />
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</ItemGroup>
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</Project>
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</Project>

‎tests/Integration.Test/Common/DicomExtensions.cs

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@@ -0,0 +1,59 @@
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// Copyright 2022 MONAI Consortium
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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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// http://www.apache.org/licenses/LICENSE-2.0
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// Unless required by applicable law or agreed to in writing, software
7+
// 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.
11+
// Licensed to the .NET Foundation under one or more agreements.
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// The .NET Foundation licenses this file to you under the MIT license.
13+
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using System.Security.Cryptography;
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using System.Text;
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using FellowOakDicom;
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using FellowOakDicom.Imaging;
18+
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namespace Monai.Deploy.InformaticsGateway.Integration.Test.Common
20+
{
21+
internal static class DicomExtensions
22+
{
23+
public static string GenerateFileName(this DicomFile dicomFile) => $"{dicomFile.Dataset.GetString(DicomTag.PatientID)}-{dicomFile.Dataset.GetString(DicomTag.SOPInstanceUID)}.dcm";
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25+
public static string CalculateHash(this DicomFile dicomFile)
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{
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var bytes = new List<byte>();
28+
var data = dicomFile.Dataset.GetSingleStringValueAsBytes(DicomTag.PatientID);
29+
bytes.AddRange(data);
30+
data = dicomFile.Dataset.GetSingleStringValueAsBytes(DicomTag.StudyInstanceUID);
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bytes.AddRange(data);
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data = dicomFile.Dataset.GetSingleStringValueAsBytes(DicomTag.SeriesInstanceUID);
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bytes.AddRange(data);
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data = dicomFile.Dataset.GetSingleStringValueAsBytes(DicomTag.SOPInstanceUID);
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bytes.AddRange(data);
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var pixelData = DicomPixelData.Create(dicomFile.Dataset);
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for (int frame = 0; frame < pixelData.NumberOfFrames; frame++)
39+
{
40+
var buffer = pixelData.GetFrame(frame);
41+
bytes.AddRange(buffer.Data);
42+
}
43+
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using var sha256Hash = SHA256.Create();
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var hash = sha256Hash.ComputeHash(bytes.ToArray());
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var sb = new StringBuilder();
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foreach(var b in hash)
48+
{
49+
sb.Append(b.ToString("X2"));
50+
}
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return sb.ToString();
52+
}
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public static byte[] GetSingleStringValueAsBytes(this DicomDataset dicomDataset, DicomTag dicomTag)
55+
{
56+
return Encoding.UTF8.GetBytes(dicomDataset.GetString(dicomTag));
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}
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}
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}

‎tests/Integration.Test/Common/Extensions.cs

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@@ -21,5 +21,18 @@ public static long NextLong(this Random random, long minValue, long maxValue)
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return (Math.Abs(longRand % (maxValue - minValue)) + minValue);
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}
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public static async Task<bool> WaitUntil(Func<bool> condition, TimeSpan timeout, int frequency = 250)
26+
{
27+
var waitTask = Task.Run(async () =>
28+
{
29+
while (!condition())
30+
{
31+
await Task.Delay(frequency);
32+
}
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});
34+
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return waitTask == await Task.WhenAny(waitTask, Task.Delay(timeout));
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}
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}
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}

‎tests/Integration.Test/Drivers/Configurations.cs

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@@ -112,6 +112,11 @@ public class TestRunnerSettings
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/// </summary>
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/// <value></value>
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public string HostIp { get; set; }
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/// <summary>
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/// Gets or sets the name of the bucket test files are uploaded to.
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/// </summary>
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public string Bucket { get; set; }
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}
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public class InformaticsGatewaySettings

‎tests/Integration.Test/Drivers/DicomInstanceGenerator.cs

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@@ -119,7 +119,7 @@ public StudyGenerationSpecs Generate(string patientId, int studiesPerPatient, in
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if (studySpec is null) throw new ArgumentNullException(nameof(studySpec));
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121121
var instancesPerSeries = _random.Next(studySpec.InstanceMin, studySpec.InstanceMax);
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var uniqueInstances = new HashSet<string>();
123123
var files = new List<DicomFile>();
124124
DicomFile dicomFile = null;
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@@ -136,6 +136,10 @@ public StudyGenerationSpecs Generate(string patientId, int studiesPerPatient, in
136136
var size = _random.NextLong(studySpec.SizeMinBytes, studySpec.SizeMaxBytes);
137137
dicomFile = generator.GenerateNewInstance(size);
138138
files.Add(dicomFile);
139+
if(!uniqueInstances.Add(dicomFile.Dataset.GetString(DicomTag.SOPInstanceUID)))
140+
{
141+
throw new Exception("Instance UID already exists, something's wrong here.");
142+
}
139143
}
140144
}
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_outputHelper.WriteLine("DICOM Instance: PID={0}, STUDY={1}",

‎tests/Integration.Test/Drivers/DicomScp.cs

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// Copyright 2022 MONAI Consortium
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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.
4+
// You may obtain a copy of the License at
5+
// http://www.apache.org/licenses/LICENSE-2.0
6+
// Unless required by applicable law or agreed to in writing, software
7+
// distributed under the License is distributed on an "AS IS" BASIS,
8+
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
9+
// See the License for the specific language governing permissions and
10+
// limitations under the License.
11+
12+
using System.Diagnostics;
13+
using System.Linq;
14+
using System.Text;
15+
using FellowOakDicom;
16+
using FellowOakDicom.Imaging.Codec;
17+
using FellowOakDicom.Log;
18+
using FellowOakDicom.Network;
19+
using FellowOakDicom.Network.Client;
20+
using Monai.Deploy.InformaticsGateway.Integration.Test.Common;
21+
using TechTalk.SpecFlow.Infrastructure;
22+
23+
namespace Monai.Deploy.InformaticsGateway.Integration.Test.Drivers
24+
{
25+
public class ServerData
26+
{
27+
public FeatureContext Context { get; set; }
28+
public Dictionary<string, string> Instances { get; set; } = new Dictionary<string, string>();
29+
public ISpecFlowOutputHelper OutputHelper {get;set;}
30+
}
31+
32+
internal class CStoreScp : DicomService, IDicomServiceProvider, IDicomCStoreProvider
33+
{
34+
private static readonly Object SyncLock = new Object();
35+
internal static readonly string PayloadsRoot = "./payloads";
36+
37+
public CStoreScp(INetworkStream stream, Encoding fallbackEncoding, ILogger log, ILogManager logManager, INetworkManager network, ITranscoderManager transcoder)
38+
: base(stream, fallbackEncoding, log, logManager, network, transcoder)
39+
{
40+
}
41+
42+
public void OnConnectionClosed(Exception exception)
43+
{
44+
if (exception is not null)
45+
{
46+
Console.WriteLine("Connection closed with error {0}.", exception);
47+
}
48+
else
49+
{
50+
Console.WriteLine("Connection closed.");
51+
}
52+
}
53+
54+
public Task<DicomCStoreResponse> OnCStoreRequestAsync(DicomCStoreRequest request)
55+
{
56+
var data = UserState as ServerData;
57+
58+
if (data == null)
59+
{
60+
throw new Exception("UserState is not instance of ServerData.");
61+
}
62+
63+
try
64+
{
65+
var key = request.File.GenerateFileName();
66+
lock(SyncLock)
67+
{
68+
data.Instances.Add(key, request.File.CalculateHash());
69+
}
70+
data.OutputHelper.WriteLine("Instance received {0}", key);
71+
72+
return Task.FromResult(new DicomCStoreResponse(request, DicomStatus.Success));
73+
}
74+
catch (Exception ex)
75+
{
76+
data.OutputHelper.WriteLine("Exception 'OnCStoreRequestAsync': {0}", ex);
77+
return Task.FromResult(new DicomCStoreResponse(request, DicomStatus.ProcessingFailure));
78+
}
79+
}
80+
81+
public Task OnCStoreRequestExceptionAsync(string tempFileName, Exception e)
82+
{
83+
Console.WriteLine("Exception 'OnCStoreRequestExceptionAsync': {0}", e);
84+
return Task.CompletedTask;
85+
}
86+
87+
public void OnReceiveAbort(DicomAbortSource source, DicomAbortReason reason)
88+
{
89+
Console.WriteLine("Exception 'OnReceiveAbort': source {0}, reason {1]", source, reason);
90+
}
91+
92+
public Task OnReceiveAssociationReleaseRequestAsync()
93+
{
94+
return SendAssociationReleaseResponseAsync();
95+
}
96+
97+
public Task OnReceiveAssociationRequestAsync(DicomAssociation association)
98+
{
99+
foreach (var pc in association.PresentationContexts)
100+
{
101+
if (pc.AbstractSyntax.StorageCategory != DicomStorageCategory.None)
102+
{
103+
pc.AcceptTransferSyntaxes(pc.GetTransferSyntaxes().ToArray());
104+
}
105+
}
106+
107+
return SendAssociationAcceptAsync(association);
108+
}
109+
110+
}
111+
}

‎tests/Integration.Test/Drivers/DicomScu.cs

Lines changed: 1 addition & 6 deletions
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@@ -52,7 +52,7 @@ public async Task<DicomStatus> CEcho(string host, int port, string callingAeTitl
5252
}
5353
catch (DicomAssociationRejectedException ex)
5454
{
55-
Console.WriteLine("Association Rejected: {0}", ex.Message);
55+
_outputHelper.WriteLine("Association Rejected: {0}", ex.Message);
5656
return DicomStatus.Cancel;
5757
}
5858
}
@@ -67,11 +67,6 @@ public async Task<DicomStatus> CStore(string host, int port, string callingAeTit
6767
var failureStatus = new List<DicomStatus>();
6868
foreach (var file in dicomFiles)
6969
{
70-
// _outputHelper.WriteLine("Sending DICOM Instance: PID={0}, STUDY={1}, SOP={2}",
71-
// file.Dataset.GetSingleValueOrDefault(DicomTag.PatientID, "N/A"),
72-
// file.Dataset.GetSingleValueOrDefault(DicomTag.StudyInstanceUID, "N/A"),
73-
// file.Dataset.GetSingleValueOrDefault(DicomTag.SOPInstanceUID, "N/A"));
74-
7570
var cStoreRequest = new DicomCStoreRequest(file);
7671
cStoreRequest.OnResponseReceived += (DicomCStoreRequest request, DicomCStoreResponse response) =>
7772
{

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