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adding HL7 message plugin support
Signed-off-by: Neil South <[email protected]>
1 parent f46262e commit 18fbfb7

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66 files changed

+1455
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‎.github/workflows/ci.yml

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@@ -183,11 +183,11 @@ jobs:
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ports:
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- 27017:27017
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steps:
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- name: Set up JDK 11
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- name: Set up JDK 17
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uses: actions/setup-java@v3
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with:
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distribution: zulu
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java-version: '11'
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java-version: '17'
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- uses: actions/setup-dotnet@v3
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with:

‎src/Api/Hl7ApplicationConfigEntity.cs

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@@ -26,7 +26,7 @@
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namespace Monai.Deploy.InformaticsGateway.Api
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{
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public class Hl7ApplicationConfigEntity : MongoDBEntityBase
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public sealed class Hl7ApplicationConfigEntity : MongoDBEntityBase
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{
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/// <summary>
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/// Gets or sets the name of a Hl7 application entity.
@@ -60,6 +60,8 @@ public class Hl7ApplicationConfigEntity : MongoDBEntityBase
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/// </summary>
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public List<string> PlugInAssemblies { get; set; } = default!;
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63+
public DateTime LastModified { get; set; } = DateTime.UtcNow;
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public IEnumerable<string> Validate()
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{
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var errors = new List<string>();
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}
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//string key, string value
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public class StringKeyValuePair : IKeyValuePair<string, string>
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public sealed class StringKeyValuePair : IKeyValuePair<string, string>, IEquatable<StringKeyValuePair>
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{
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[Key]
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public string Key { get; set; } = string.Empty;
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137139
}
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public class DataKeyValuePair : IKeyValuePair<string, DataLinkType>
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public sealed class DataKeyValuePair : IKeyValuePair<string, DataLinkType>, IEquatable<DataKeyValuePair>
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{
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[Key]
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public string Key { get; set; } = string.Empty;

‎src/InformaticsGateway/Services/HealthLevel7/IMllpClient.cs renamed to ‎src/Api/Mllp/IMllpClient.cs

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using System.Threading;
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using System.Threading.Tasks;
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namespace Monai.Deploy.InformaticsGateway.Services.HealthLevel7
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namespace Monai.Deploy.InformaticsGateway.Api.Mllp
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{
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internal interface IMllpClient : IDisposable
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public interface IMllpClient : IDisposable
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{
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Guid ClientId { get; }
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2727
string ClientIp { get; }
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Task Start(Func<IMllpClient, MllpClientResult, Task> onDisconnect, CancellationToken cancellationToken);
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}
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}
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}

‎src/InformaticsGateway/Services/HealthLevel7/IMllpExtract.cs renamed to ‎src/Api/Mllp/IMllpExtract.cs

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using HL7.Dotnetcore;
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using Monai.Deploy.InformaticsGateway.Api.Storage;
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namespace Monai.Deploy.InformaticsGateway.Services.HealthLevel7
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namespace Monai.Deploy.InformaticsGateway.Api.Mllp
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{
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internal interface IMllpExtract
24+
public interface IMllpExtract
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{
26-
Task<Message> ExtractInfo(Hl7FileStorageMetadata meta, Message message);
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Task<Message> ExtractInfo(Hl7FileStorageMetadata meta, Message message, Hl7ApplicationConfigEntity configItem);
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Task<Hl7ApplicationConfigEntity?> GetConfigItem(Message message);
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}
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}

‎src/InformaticsGateway/Services/HealthLevel7/IMllpService.cs renamed to ‎src/Api/Mllp/IMllpService.cs

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using System.Threading;
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using System.Threading.Tasks;
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namespace Monai.Deploy.InformaticsGateway.Services.HealthLevel7
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namespace Monai.Deploy.InformaticsGateway.Api.Mllp
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{
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public interface IMllpService
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{

‎src/InformaticsGateway/Services/HealthLevel7/MllpClientResult.cs renamed to ‎src/Api/Mllp/MllpClientResult.cs

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using System.Collections.Generic;
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using HL7.Dotnetcore;
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namespace Monai.Deploy.InformaticsGateway.Services.HealthLevel7
21+
namespace Monai.Deploy.InformaticsGateway.Api.Mllp
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{
23-
internal class MllpClientResult
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public class MllpClientResult
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{
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public IList<Message> Messages { get; }
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public AggregateException? AggregateException { get; }

‎src/Api/Monai.Deploy.InformaticsGateway.Api.csproj

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<ItemGroup>
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<PackageReference Include="fo-dicom" Version="5.1.1" />
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<PackageReference Include="HL7-dotnetcore" Version="2.36.0" />
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<PackageReference Include="Macross.Json.Extensions" Version="3.0.0" />
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<PackageReference Include="Microsoft.EntityFrameworkCore.Abstractions" Version="6.0.25" />
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<PackageReference Include="Monai.Deploy.Messaging" Version="1.0.5" />

‎src/Api/PlugIns/IInputHL7DataPlugIn.cs

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/*
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* Copyright 2023 MONAI Consortium
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*
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* Licensed under the Apache License, Version 2.0 (the "License");
5+
* you may not use this file except in compliance with the License.
6+
* You may obtain a copy of the License at
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*
8+
* 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
11+
* distributed under the License is distributed on an "AS IS" BASIS,
12+
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
13+
* See the License for the specific language governing permissions and
14+
* limitations under the License.
15+
*/
16+
17+
using System.Threading.Tasks;
18+
using HL7.Dotnetcore;
19+
using Monai.Deploy.InformaticsGateway.Api.Storage;
20+
21+
namespace Monai.Deploy.InformaticsGateway.Api.PlugIns
22+
{
23+
/// <summary>
24+
/// <c>IInputDataPlugIn</c> enables lightweight data processing over incoming data received from supported data ingestion
25+
/// services.
26+
/// Refer to <see cref="IInputHL7DataPlugInEngine" /> for additional details.
27+
/// </summary>
28+
public interface IInputHL7DataPlugIn
29+
{
30+
string Name { get; }
31+
32+
Task<(Message hl7Message, FileStorageMetadata fileMetadata)> ExecuteAsync(Message hl7File, FileStorageMetadata fileMetadata);
33+
}
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35+
}

‎src/Api/PlugIns/IInputHL7DataPlugInEngine.cs

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/*
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* Copyright 2023 MONAI Consortium
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*
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* Licensed under the Apache License, Version 2.0 (the "License");
5+
* you may not use this file except in compliance with the License.
6+
* You may obtain a copy of the License at
7+
*
8+
* http://www.apache.org/licenses/LICENSE-2.0
9+
*
10+
* Unless required by applicable law or agreed to in writing, software
11+
* distributed under the License is distributed on an "AS IS" BASIS,
12+
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
13+
* See the License for the specific language governing permissions and
14+
* limitations under the License.
15+
*/
16+
17+
using System;
18+
using System.Collections.Generic;
19+
using System.Threading.Tasks;
20+
using HL7.Dotnetcore;
21+
using Monai.Deploy.InformaticsGateway.Api.Storage;
22+
23+
namespace Monai.Deploy.InformaticsGateway.Api.PlugIns
24+
{
25+
/// <summary>
26+
/// <c>IInputDataPlugInEngine</c> processes incoming data receivied from various supported services through
27+
/// a list of plug-ins based on <see cref="IInputDataPlugIn"/>.
28+
/// Rules:
29+
/// <list type="bullet">
30+
/// <item>SCP: A list of plug-ins can be configured with each AET, and each plug-in is executed in the order stored, enabling piping of the incoming data before each file is uploaded to the storage service.</item>
31+
/// <item>Incoming data is processed one file at a time and SHALL not wait for the entire study to arrive.</item>
32+
/// <item>Plug-ins MUST be lightweight and not hinder the upload process.</item>
33+
/// <item>Plug-ins SHALL not accumulate files in memory or storage for bulk processing.</item>
34+
/// </list>
35+
/// </summary>
36+
public interface IInputHL7DataPlugInEngine
37+
{
38+
void Configure(IReadOnlyList<string> pluginAssemblies);
39+
40+
Task<Tuple<Message, FileStorageMetadata>> ExecutePlugInsAsync(Message hl7File, FileStorageMetadata fileMetadata, Hl7ApplicationConfigEntity configItem);
41+
}
42+
}

‎src/Api/Storage/Hl7FileStorageMetadata.cs

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public sealed record Hl7FileStorageMetadata : FileStorageMetadata
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{
2929
public const string Hl7SubDirectoryName = "ehr";
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public const string FileExtension = ".txt";
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public const string FileExtension = ".hl7";
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/// <inheritdoc/>
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[JsonIgnore]

‎src/Api/Test/packages.lock.json

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"System.Threading.Channels": "6.0.0"
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}
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},
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"HL7-dotnetcore": {
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"type": "Transitive",
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"resolved": "2.36.0",
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"contentHash": "N1HLMeIqYuY+4O69ItgZJoDBnnpNkK5N2pClceTJ2nFJxsP48iCsA4iz3tm43Yszi4r/vaThoc3UoLBfGP3vKw=="
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},
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"Macross.Json.Extensions": {
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"dependencies": {
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"HL7-dotnetcore": "[2.36.0, )",
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"Macross.Json.Extensions": "[3.0.0, )",
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"Microsoft.EntityFrameworkCore.Abstractions": "[6.0.25, )",
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"Monai.Deploy.InformaticsGateway.Common": "[1.0.0, )",

‎src/Api/packages.lock.json

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"System.Threading.Channels": "6.0.0"
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}
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"HL7-dotnetcore": {
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"type": "Direct",
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"requested": "[2.36.0, )",
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"resolved": "2.36.0",
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"contentHash": "N1HLMeIqYuY+4O69ItgZJoDBnnpNkK5N2pClceTJ2nFJxsP48iCsA4iz3tm43Yszi4r/vaThoc3UoLBfGP3vKw=="
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},
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‎src/CLI/Test/packages.lock.json

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"resolved": "2.36.0",
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"contentHash": "N1HLMeIqYuY+4O69ItgZJoDBnnpNkK5N2pClceTJ2nFJxsP48iCsA4iz3tm43Yszi4r/vaThoc3UoLBfGP3vKw=="
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},
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‎src/CLI/packages.lock.json

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"resolved": "2.36.0",
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"contentHash": "N1HLMeIqYuY+4O69ItgZJoDBnnpNkK5N2pClceTJ2nFJxsP48iCsA4iz3tm43Yszi4r/vaThoc3UoLBfGP3vKw=="
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},
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"HL7-dotnetcore": "[2.36.0, )",
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"Microsoft.EntityFrameworkCore.Abstractions": "[6.0.25, )",
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‎src/Client/Test/packages.lock.json

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"HL7-dotnetcore": "[2.36.0, )",
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‎src/Client/packages.lock.json

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"HL7-dotnetcore": {
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"resolved": "2.36.0",
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"contentHash": "N1HLMeIqYuY+4O69ItgZJoDBnnpNkK5N2pClceTJ2nFJxsP48iCsA4iz3tm43Yszi4r/vaThoc3UoLBfGP3vKw=="
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},
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"Macross.Json.Extensions": {
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"monai.deploy.informaticsgateway.api": {
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"dependencies": {
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"HL7-dotnetcore": "[2.36.0, )",
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"Microsoft.EntityFrameworkCore.Abstractions": "[6.0.25, )",
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"Monai.Deploy.InformaticsGateway.Common": "[1.0.0, )",

‎src/Configuration/Test/packages.lock.json

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"System.Threading.Channels": "6.0.0"
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"HL7-dotnetcore": {
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"type": "Transitive",
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"resolved": "2.36.0",
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"contentHash": "N1HLMeIqYuY+4O69ItgZJoDBnnpNkK5N2pClceTJ2nFJxsP48iCsA4iz3tm43Yszi4r/vaThoc3UoLBfGP3vKw=="
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},
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"monai.deploy.informaticsgateway.api": {
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"dependencies": {
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"HL7-dotnetcore": "[2.36.0, )",
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"Macross.Json.Extensions": "[3.0.0, )",
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"Microsoft.EntityFrameworkCore.Abstractions": "[6.0.25, )",
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"Monai.Deploy.InformaticsGateway.Common": "[1.0.0, )",

‎src/Configuration/packages.lock.json

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"System.Threading.Channels": "6.0.0"
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"HL7-dotnetcore": {
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"type": "Transitive",
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"resolved": "2.36.0",
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"contentHash": "N1HLMeIqYuY+4O69ItgZJoDBnnpNkK5N2pClceTJ2nFJxsP48iCsA4iz3tm43Yszi4r/vaThoc3UoLBfGP3vKw=="
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},
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"Macross.Json.Extensions": {
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"monai.deploy.informaticsgateway.api": {
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"dependencies": {
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"HL7-dotnetcore": "[2.36.0, )",
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"Macross.Json.Extensions": "[3.0.0, )",
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"Microsoft.EntityFrameworkCore.Abstractions": "[6.0.25, )",
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"Monai.Deploy.InformaticsGateway.Common": "[1.0.0, )",

‎src/Database/Api/Test/packages.lock.json

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"HL7-dotnetcore": {
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"resolved": "2.36.0",
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"contentHash": "N1HLMeIqYuY+4O69ItgZJoDBnnpNkK5N2pClceTJ2nFJxsP48iCsA4iz3tm43Yszi4r/vaThoc3UoLBfGP3vKw=="
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‎src/Database/Api/packages.lock.json

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"contentHash": "N1HLMeIqYuY+4O69ItgZJoDBnnpNkK5N2pClceTJ2nFJxsP48iCsA4iz3tm43Yszi4r/vaThoc3UoLBfGP3vKw=="
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‎src/Database/DatabaseMigrationManager.cs

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var matchingTypes = new List<Type>();
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foreach (var assembly in assemblies)
6363
{
64-
var types = assembly.ExportedTypes.Where(p => p.IsAssignableFrom(typeof(IDatabaseMigrationManager)));
64+
var types = assembly.ExportedTypes.Where(p => p.IsAssignableFrom(typeof(IDatabaseMigrationManager)) && p.Name != nameof(IDatabaseMigrationManager));
6565
if (types.Any())
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{
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‎src/Database/EntityFramework/Migrations/20231204113501_Hl7DEstinationAndConfig.cs

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using System;
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using Microsoft.EntityFrameworkCore.Migrations;
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#nullable disable

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