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gh-435 Fix CLI to read log dir path from NLog config file (#436)
* gh-435 Fix CLI to read log dir path from NLog config file * Update changelog * Add/update unit tests Signed-off-by: Victor Chang <[email protected]>
1 parent d54788e commit 0ff1963

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‎docs/changelog.md

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# Changelog
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## 0.4.0
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[GitHub Milestone 0.4.0](https://github.com/Project-MONAI/monai-deploy-informatics-gateway/milestone/5)
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- gh-435 Fix CLI to read log dir path from NLog config file.
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## 0.3.21
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[GitHub Milestone 0.3.21](https://github.com/Project-MONAI/monai-deploy-informatics-gateway/milestone/26)
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- Remove the need to double copy files to storage service.
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## 0.3.20
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[GitHub Milestone 0.3.20](https://github.com/Project-MONAI/monai-deploy-informatics-gateway/milestone/25)
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- gh-396 Spawn new thread for processing echo requests.
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## 0.3.19
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[GitHub Milestone 0.3.19](https://github.com/Project-MONAI/monai-deploy-informatics-gateway/milestone/24)
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- gh-392 Fix GET /config/aetitle URL.
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## 0.3.18
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[GitHub Milestone 0.3.18](https://github.com/Project-MONAI/monai-deploy-informatics-gateway/milestone/23)
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- gh-390 New API to retrieve registered source AETs.
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## 0.3.11
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[GitHub Milestone 0.3.17](https://github.com/Project-MONAI/monai-deploy-informatics-gateway/milestone/22)
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- gh-385 Resets ActionBlock if faulted or cancelled in Payload assembler pipeline.
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## 0.3.16
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[GitHub Milestone 0.3.16](https://github.com/Project-MONAI/monai-deploy-informatics-gateway/milestone/21)

‎src/CLI/Logging/Log.cs

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@@ -133,8 +133,8 @@ public static partial class Log
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[LoggerMessage(EventId = 30043, Level = LogLevel.Debug, Message = "Available manifest names {names}.")]
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public static partial void AvailableManifest(this ILogger logger, string names);
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[LoggerMessage(EventId = 30044, Level = LogLevel.Information, Message = "Saving appsettings.json to {path}.")]
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public static partial void SaveAppSettings(this ILogger logger, string path);
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[LoggerMessage(EventId = 30044, Level = LogLevel.Information, Message = "Saving {resource} to {path}.")]
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public static partial void SaveAppSettings(this ILogger logger, string resource, string path);
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[LoggerMessage(EventId = 30045, Level = LogLevel.Information, Message = "{path} updated successfully.")]
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public static partial void AppSettingUpdated(this ILogger logger, string path);

‎src/CLI/Monai.Deploy.InformaticsGateway.CLI.csproj

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@@ -51,6 +51,7 @@
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<ItemGroup>
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<EmbeddedResource Include="..\InformaticsGateway\appsettings.json" Link="Resources\appsettings.json" />
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<EmbeddedResource Include="..\InformaticsGateway\nlog.config" Link="Resources\nlog.config" />
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</ItemGroup>
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<ItemGroup>

‎src/CLI/Options/Common.cs

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@@ -25,9 +25,12 @@ public static class Common
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public static readonly string MigDirectory = Path.Combine(HomeDir, ".mig");
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public static readonly string ContainerApplicationRootPath = "/opt/monai/ig";
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public static readonly string MountedConfigFilePath = Path.Combine(ContainerApplicationRootPath, "appsettings.json");
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public static readonly string MountedNLogConfigFilePath = Path.Combine(ContainerApplicationRootPath, "nlog.config");
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public static readonly string MountedDatabasePath = "/database";
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public static readonly string MountedPlugInsPath = Path.Combine(ContainerApplicationRootPath, "plug-ins");
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public static readonly string ConfigFilePath = Path.Combine(MigDirectory, "appsettings.json");
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public static readonly string NLogConfigFilePath = Path.Combine(MigDirectory, "nlog.config");
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public static readonly string AppSettingsResourceName = $"{typeof(Program).Namespace}.Resources.appsettings.json";
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public static readonly string NLogConfigResourceName = $"{typeof(Program).Namespace}.Resources.nlog.config";
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}
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}

‎src/CLI/Program.cs

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@@ -63,6 +63,8 @@ internal static Parser BuildParser()
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services.AddScoped<IFileSystem, FileSystem>();
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services.AddScoped<IConfirmationPrompt, ConfirmationPrompt>();
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services.AddScoped<IConsoleRegion, ConsoleRegion>();
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services.AddScoped<IConfigurationOptionAccessor, ConfigurationOptionAccessor>();
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services.AddScoped<INLogConfigurationOptionAccessor, NLogConfigurationOptionAccessor>();
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services.AddHttpClient<InformaticsGatewayClient>();
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services.AddSingleton<IInformaticsGatewayClient>(p => p.GetRequiredService<InformaticsGatewayClient>());
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services.AddSingleton<IConfigurationService, ConfigurationService>();

‎src/CLI/Properties/launchSettings.json

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@@ -2,7 +2,7 @@
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"profiles": {
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"Monai.Deploy.InformaticsGateway.CLI": {
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"commandName": "Project",
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"commandLineArgs": "aet add -a Test"
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"commandLineArgs": "start"
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}
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}
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}

‎src/CLI/Services/ConfigurationOptionAccessor.cs

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/*
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* Copyright 2021-2022 MONAI Consortium
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* Copyright 2021-2023 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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/// </summary>
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Uri InformaticsGatewayServerUri { get; }
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/// <summary>
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/// Gets the log storage path from appsettings.json.
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/// </summary>
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string LogStoragePath { get; }
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/// <summary>
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/// Gets or set the type of container runner from appsettings.json.
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/// </summary>
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public ConfigurationOptionAccessor(IFileSystem fileSystem)
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{
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_fileSystem = fileSystem;
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_fileSystem = fileSystem ?? throw new ArgumentNullException(nameof(fileSystem));
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}
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public int DicomListeningPort
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}
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}
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public string LogStoragePath
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{
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get
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{
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var logPath = GetValueFromJsonPath<string>("Logging.File.BasePath");
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if (logPath.StartsWith("/"))
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{
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return logPath;
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}
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return _fileSystem.Path.Combine(Common.ContainerApplicationRootPath, logPath);
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}
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}
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public Runner Runner
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{
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get
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{
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get
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{
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return GetValueFromJsonPath<string>("InformaticsGateway.storage.temporary");
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return GetValueFromJsonPath<string>("InformaticsGateway.storage.localTemporaryStoragePath");
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}
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}
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‎src/CLI/Services/ConfigurationService.cs

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/*
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* Copyright 2021-2022 MONAI Consortium
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* Copyright 2021-2023 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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using System.Reflection;
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using System.Threading;
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using System.Threading.Tasks;
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using Ardalis.GuardClauses;
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using Microsoft.Extensions.Logging;
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namespace Monai.Deploy.InformaticsGateway.CLI.Services
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public bool IsConfigExists => _fileSystem.File.Exists(Common.ConfigFilePath);
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public IConfigurationOptionAccessor Configurations { get; }
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public INLogConfigurationOptionAccessor NLogConfigurations { get; }
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public ConfigurationService(ILogger<ConfigurationService> logger, IFileSystem fileSystem, IEmbeddedResource embeddedResource)
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public ConfigurationService(
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ILogger<ConfigurationService> logger,
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IFileSystem fileSystem,
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IEmbeddedResource embeddedResource,
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IConfigurationOptionAccessor configurationOptionAccessor,
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INLogConfigurationOptionAccessor nLogConfigurationOptionAccessor)
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{
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_logger = logger ?? throw new ArgumentNullException(nameof(logger));
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_fileSystem = fileSystem ?? throw new ArgumentNullException(nameof(fileSystem));
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_embeddedResource = embeddedResource ?? throw new ArgumentNullException(nameof(embeddedResource));
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Configurations = new ConfigurationOptionAccessor(fileSystem);
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Configurations = configurationOptionAccessor ?? throw new ArgumentNullException(nameof(configurationOptionAccessor));
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NLogConfigurations = nLogConfigurationOptionAccessor ?? throw new ArgumentNullException(nameof(nLogConfigurationOptionAccessor));
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}
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public void CreateConfigDirectoryIfNotExist()
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public async Task Initialize(CancellationToken cancellationToken)
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{
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_logger.DebugMessage("Reading default application configurations...");
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using var stream = _embeddedResource.GetManifestResourceStream(Common.AppSettingsResourceName);
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await WriteConfigFile(Common.AppSettingsResourceName, Common.ConfigFilePath, cancellationToken).ConfigureAwait(false);
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await WriteConfigFile(Common.NLogConfigResourceName, Common.NLogConfigFilePath, cancellationToken).ConfigureAwait(false);
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}
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public async Task WriteConfigFile(string resourceName, string outputPath, CancellationToken cancellationToken)
71+
{
72+
Guard.Against.NullOrWhiteSpace(resourceName, nameof(resourceName));
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Guard.Against.NullOrWhiteSpace(outputPath, nameof(outputPath));
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using var stream = _embeddedResource.GetManifestResourceStream(resourceName);
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if (stream is null)
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{
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_logger.AvailableManifest(string.Join(",", Assembly.GetExecutingAssembly().GetManifestResourceNames()));
63-
throw new ConfigurationException($"Default configuration file could not be loaded, please reinstall the CLI.");
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throw new ConfigurationException($"Default configuration file: {resourceName} could not be loaded, please reinstall the CLI.");
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}
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CreateConfigDirectoryIfNotExist();
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67-
_logger.SaveAppSettings(Common.ConfigFilePath);
68-
using (var fileStream = _fileSystem.FileStream.Create(Common.ConfigFilePath, FileMode.Create))
84+
_logger.SaveAppSettings(resourceName, outputPath);
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using (var fileStream = _fileSystem.FileStream.Create(outputPath, FileMode.Create))
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{
7087
await stream.CopyToAsync(fileStream, cancellationToken).ConfigureAwait(false);
7188
await fileStream.FlushAsync(cancellationToken).ConfigureAwait(false);
7289
}
73-
_logger.AppSettingUpdated(Common.ConfigFilePath);
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_logger.AppSettingUpdated(outputPath);
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}
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}
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}

‎src/CLI/Services/DockerRunner.cs

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/*
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* Copyright 2021-2022 MONAI Consortium
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* Copyright 2021-2023 MONAI Consortium
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*
44
* 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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114114
};
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createContainerParams.HostConfig.PortBindings = new Dictionary<string, IList<PortBinding>>();
117+
createContainerParams.HostConfig.NetworkMode = "monaideploy";
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_logger.DockerPrtBinding(_configurationService.Configurations.DicomListeningPort);
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createContainerParams.ExposedPorts.Add($"{_configurationService.Configurations.DicomListeningPort}/tcp", new EmptyStruct());
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_fileSystem.Directory.CreateDirectoryIfNotExists(_configurationService.Configurations.HostDatabaseStorageMount);
136137
createContainerParams.HostConfig.Mounts.Add(new Mount { Type = "bind", ReadOnly = false, Source = _configurationService.Configurations.HostDatabaseStorageMount, Target = Common.MountedDatabasePath });
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138-
_logger.DockerMountAppLogs(_configurationService.Configurations.HostLogsStorageMount, _configurationService.Configurations.LogStoragePath);
139+
_logger.DockerMountAppLogs(_configurationService.Configurations.HostLogsStorageMount, _configurationService.NLogConfigurations.LogStoragePath);
139140
_fileSystem.Directory.CreateDirectoryIfNotExists(_configurationService.Configurations.HostLogsStorageMount);
140-
createContainerParams.HostConfig.Mounts.Add(new Mount { Type = "bind", ReadOnly = false, Source = _configurationService.Configurations.HostLogsStorageMount, Target = _configurationService.Configurations.LogStoragePath });
141+
createContainerParams.HostConfig.Mounts.Add(new Mount { Type = "bind", ReadOnly = false, Source = _configurationService.Configurations.HostLogsStorageMount, Target = _configurationService.NLogConfigurations.LogStoragePath });
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142143
_logger.DockerMountPlugins(_configurationService.Configurations.HostPlugInsStorageMount, Common.MountedPlugInsPath);
143144
_fileSystem.Directory.CreateDirectoryIfNotExists(_configurationService.Configurations.HostPlugInsStorageMount);

‎src/CLI/Services/EmbeddedResource.cs

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@@ -29,7 +29,8 @@ public class EmbeddedResource : IEmbeddedResource
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public Stream GetManifestResourceStream(string name)
3030
{
3131
Guard.Against.NullOrWhiteSpace(name, nameof(name));
32-
return GetType().Assembly.GetManifestResourceStream(Common.AppSettingsResourceName);
32+
33+
return GetType().Assembly.GetManifestResourceStream(name);
3334
}
3435
}
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}

‎src/CLI/Services/IConfigurationService.cs

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/// </summary>
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IConfigurationOptionAccessor Configurations { get; }
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/// <summary>
30+
/// Gets the configurations inside nlog.config
31+
/// </summary>
32+
INLogConfigurationOptionAccessor NLogConfigurations { get; }
33+
2934
/// <summary>
3035
/// Gets whether the configuration file exists or not.
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/// </summary>

‎src/CLI/Services/NLogConfigurationOptionAccessor.cs

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/*
2+
* Copyright 2023 MONAI Consortium
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*
4+
* 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.IO.Abstractions;
19+
using System.Xml;
20+
21+
namespace Monai.Deploy.InformaticsGateway.CLI.Services
22+
{
23+
public interface INLogConfigurationOptionAccessor
24+
{
25+
/// <summary>
26+
/// Gets the logs directory path.
27+
/// </summary>
28+
string LogStoragePath { get; }
29+
}
30+
31+
public class NLogConfigurationOptionAccessor : INLogConfigurationOptionAccessor
32+
{
33+
private readonly XmlDocument _xmlDocument;
34+
private readonly XmlNamespaceManager _namespaceManager;
35+
36+
public NLogConfigurationOptionAccessor(IFileSystem fileSystem)
37+
{
38+
if (fileSystem is null)
39+
{
40+
throw new ArgumentNullException(nameof(fileSystem));
41+
}
42+
43+
var xml = fileSystem.File.ReadAllText(Common.NLogConfigFilePath);
44+
_xmlDocument = new XmlDocument();
45+
_xmlDocument.LoadXml(xml);
46+
_namespaceManager = new XmlNamespaceManager(_xmlDocument.NameTable);
47+
_namespaceManager.AddNamespace("ns", "http://www.nlog-project.org/schemas/NLog.xsd");
48+
}
49+
50+
public string LogStoragePath
51+
{
52+
get
53+
{
54+
var value = _xmlDocument.SelectSingleNode("//ns:variable[@name='logDir']/@value", _namespaceManager).InnerText;
55+
value = value.Replace("${basedir}", Common.ContainerApplicationRootPath);
56+
return value;
57+
}
58+
}
59+
}
60+
}

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