gh-435 Fix CLI to read log dir path from NLog config file (#436)

mocsharp · web-flow · commit 0ff1963d1942 · 2023-08-10T10:46:12.000-07:00
* gh-435 Fix CLI to read log dir path from NLog config file * Update changelog * Add/update unit tests Signed-off-by: Victor Chang <vicchang@nvidia.com>
diff --git a/docs/changelog.md b/docs/changelog.md
@@ -17,6 +17,44 @@
 
 # Changelog
 
+## 0.4.0
+
+[GitHub Milestone 0.4.0](https://github.com/Project-MONAI/monai-deploy-informatics-gateway/milestone/5)
+
+- gh-435 Fix CLI to read log dir path from NLog config file.
+
+
+## 0.3.21
+
+[GitHub Milestone 0.3.21](https://github.com/Project-MONAI/monai-deploy-informatics-gateway/milestone/26)
+
+- Remove the need to double copy files to storage service.
+
+## 0.3.20
+
+[GitHub Milestone 0.3.20](https://github.com/Project-MONAI/monai-deploy-informatics-gateway/milestone/25)
+
+- gh-396 Spawn new thread for processing echo requests.
+
+## 0.3.19
+
+[GitHub Milestone 0.3.19](https://github.com/Project-MONAI/monai-deploy-informatics-gateway/milestone/24)
+
+- gh-392 Fix GET /config/aetitle URL.
+
+## 0.3.18
+
+[GitHub Milestone 0.3.18](https://github.com/Project-MONAI/monai-deploy-informatics-gateway/milestone/23)
+
+- gh-390 New API to retrieve registered source AETs.
+
+## 0.3.11
+
+[GitHub Milestone 0.3.17](https://github.com/Project-MONAI/monai-deploy-informatics-gateway/milestone/22)
+
+- gh-385 Resets ActionBlock if faulted or cancelled in Payload assembler pipeline.
+
+
 ## 0.3.16
 
 [GitHub Milestone 0.3.16](https://github.com/Project-MONAI/monai-deploy-informatics-gateway/milestone/21)
diff --git a/src/CLI/Logging/Log.cs b/src/CLI/Logging/Log.cs
@@ -133,8 +133,8 @@ public static partial class Log
         [LoggerMessage(EventId = 30043, Level = LogLevel.Debug, Message = "Available manifest names {names}.")]
         public static partial void AvailableManifest(this ILogger logger, string names);
 
-        [LoggerMessage(EventId = 30044, Level = LogLevel.Information, Message = "Saving appsettings.json to {path}.")]
-        public static partial void SaveAppSettings(this ILogger logger, string path);
+        [LoggerMessage(EventId = 30044, Level = LogLevel.Information, Message = "Saving {resource} to {path}.")]
+        public static partial void SaveAppSettings(this ILogger logger, string resource, string path);
 
         [LoggerMessage(EventId = 30045, Level = LogLevel.Information, Message = "{path} updated successfully.")]
         public static partial void AppSettingUpdated(this ILogger logger, string path);
diff --git a/src/CLI/Monai.Deploy.InformaticsGateway.CLI.csproj b/src/CLI/Monai.Deploy.InformaticsGateway.CLI.csproj
@@ -51,6 +51,7 @@
 
   <ItemGroup>
     <EmbeddedResource Include="..\InformaticsGateway\appsettings.json" Link="Resources\appsettings.json" />
+    <EmbeddedResource Include="..\InformaticsGateway\nlog.config" Link="Resources\nlog.config" />
   </ItemGroup>
 
   <ItemGroup>
diff --git a/src/CLI/Options/Common.cs b/src/CLI/Options/Common.cs
@@ -25,9 +25,12 @@ public static class Common
         public static readonly string MigDirectory = Path.Combine(HomeDir, ".mig");
         public static readonly string ContainerApplicationRootPath = "/opt/monai/ig";
         public static readonly string MountedConfigFilePath = Path.Combine(ContainerApplicationRootPath, "appsettings.json");
+        public static readonly string MountedNLogConfigFilePath = Path.Combine(ContainerApplicationRootPath, "nlog.config");
         public static readonly string MountedDatabasePath = "/database";
         public static readonly string MountedPlugInsPath = Path.Combine(ContainerApplicationRootPath, "plug-ins");
         public static readonly string ConfigFilePath = Path.Combine(MigDirectory, "appsettings.json");
+        public static readonly string NLogConfigFilePath = Path.Combine(MigDirectory, "nlog.config");
         public static readonly string AppSettingsResourceName = $"{typeof(Program).Namespace}.Resources.appsettings.json";
+        public static readonly string NLogConfigResourceName = $"{typeof(Program).Namespace}.Resources.nlog.config";
     }
 }
diff --git a/src/CLI/Program.cs b/src/CLI/Program.cs
@@ -63,6 +63,8 @@ internal static Parser BuildParser()
                                     services.AddScoped<IFileSystem, FileSystem>();
                                     services.AddScoped<IConfirmationPrompt, ConfirmationPrompt>();
                                     services.AddScoped<IConsoleRegion, ConsoleRegion>();
+                                    services.AddScoped<IConfigurationOptionAccessor, ConfigurationOptionAccessor>();
+                                    services.AddScoped<INLogConfigurationOptionAccessor, NLogConfigurationOptionAccessor>();
                                     services.AddHttpClient<InformaticsGatewayClient>();
                                     services.AddSingleton<IInformaticsGatewayClient>(p => p.GetRequiredService<InformaticsGatewayClient>());
                                     services.AddSingleton<IConfigurationService, ConfigurationService>();
diff --git a/src/CLI/Properties/launchSettings.json b/src/CLI/Properties/launchSettings.json
@@ -2,7 +2,7 @@
   "profiles": {
     "Monai.Deploy.InformaticsGateway.CLI": {
       "commandName": "Project",
-      "commandLineArgs": "aet add -a Test"
+      "commandLineArgs": "start"
     }
   }
 }
diff --git a/src/CLI/Services/ConfigurationOptionAccessor.cs b/src/CLI/Services/ConfigurationOptionAccessor.cs
@@ -1,5 +1,5 @@
 /*
- * Copyright 2021-2022 MONAI Consortium
+ * Copyright 2021-2023 MONAI Consortium
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -76,11 +76,6 @@ public interface IConfigurationOptionAccessor
         /// </summary>
         Uri InformaticsGatewayServerUri { get; }
 
-        /// <summary>
-        /// Gets the log storage path from appsettings.json.
-        /// </summary>
-        string LogStoragePath { get; }
-
         /// <summary>
         /// Gets or set the type of container runner from appsettings.json.
         /// </summary>
@@ -99,7 +94,7 @@ public class ConfigurationOptionAccessor : IConfigurationOptionAccessor
 
         public ConfigurationOptionAccessor(IFileSystem fileSystem)
         {
-            _fileSystem = fileSystem;
+            _fileSystem = fileSystem ?? throw new ArgumentNullException(nameof(fileSystem));
         }
 
         public int DicomListeningPort
@@ -223,19 +218,6 @@ public Uri InformaticsGatewayServerUri
             }
         }
 
-        public string LogStoragePath
-        {
-            get
-            {
-                var logPath = GetValueFromJsonPath<string>("Logging.File.BasePath");
-                if (logPath.StartsWith("/"))
-                {
-                    return logPath;
-                }
-                return _fileSystem.Path.Combine(Common.ContainerApplicationRootPath, logPath);
-            }
-        }
-
         public Runner Runner
         {
             get
@@ -255,7 +237,7 @@ public string TempStoragePath
         {
             get
             {
-                return GetValueFromJsonPath<string>("InformaticsGateway.storage.temporary");
+                return GetValueFromJsonPath<string>("InformaticsGateway.storage.localTemporaryStoragePath");
             }
         }
 
diff --git a/src/CLI/Services/ConfigurationService.cs b/src/CLI/Services/ConfigurationService.cs
@@ -1,5 +1,5 @@
 /*
- * Copyright 2021-2022 MONAI Consortium
+ * Copyright 2021-2023 MONAI Consortium
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -20,6 +20,7 @@
 using System.Reflection;
 using System.Threading;
 using System.Threading.Tasks;
+using Ardalis.GuardClauses;
 using Microsoft.Extensions.Logging;
 
 namespace Monai.Deploy.InformaticsGateway.CLI.Services
@@ -35,13 +36,20 @@ public class ConfigurationService : IConfigurationService
         public bool IsConfigExists => _fileSystem.File.Exists(Common.ConfigFilePath);
 
         public IConfigurationOptionAccessor Configurations { get; }
+        public INLogConfigurationOptionAccessor NLogConfigurations { get; }
 
-        public ConfigurationService(ILogger<ConfigurationService> logger, IFileSystem fileSystem, IEmbeddedResource embeddedResource)
+        public ConfigurationService(
+            ILogger<ConfigurationService> logger,
+            IFileSystem fileSystem,
+            IEmbeddedResource embeddedResource,
+            IConfigurationOptionAccessor configurationOptionAccessor,
+            INLogConfigurationOptionAccessor nLogConfigurationOptionAccessor)
         {
             _logger = logger ?? throw new ArgumentNullException(nameof(logger));
             _fileSystem = fileSystem ?? throw new ArgumentNullException(nameof(fileSystem));
             _embeddedResource = embeddedResource ?? throw new ArgumentNullException(nameof(embeddedResource));
-            Configurations = new ConfigurationOptionAccessor(fileSystem);
+            Configurations = configurationOptionAccessor ?? throw new ArgumentNullException(nameof(configurationOptionAccessor));
+            NLogConfigurations = nLogConfigurationOptionAccessor ?? throw new ArgumentNullException(nameof(nLogConfigurationOptionAccessor));
         }
 
         public void CreateConfigDirectoryIfNotExist()
@@ -55,22 +63,32 @@ public void CreateConfigDirectoryIfNotExist()
         public async Task Initialize(CancellationToken cancellationToken)
         {
             _logger.DebugMessage("Reading default application configurations...");
-            using var stream = _embeddedResource.GetManifestResourceStream(Common.AppSettingsResourceName);
+            await WriteConfigFile(Common.AppSettingsResourceName, Common.ConfigFilePath, cancellationToken).ConfigureAwait(false);
+            await WriteConfigFile(Common.NLogConfigResourceName, Common.NLogConfigFilePath, cancellationToken).ConfigureAwait(false);
+        }
+
+        public async Task WriteConfigFile(string resourceName, string outputPath, CancellationToken cancellationToken)
+        {
+            Guard.Against.NullOrWhiteSpace(resourceName, nameof(resourceName));
+            Guard.Against.NullOrWhiteSpace(outputPath, nameof(outputPath));
+
+            using var stream = _embeddedResource.GetManifestResourceStream(resourceName);
 
             if (stream is null)
             {
                 _logger.AvailableManifest(string.Join(",", Assembly.GetExecutingAssembly().GetManifestResourceNames()));
-                throw new ConfigurationException($"Default configuration file could not be loaded, please reinstall the CLI.");
+                throw new ConfigurationException($"Default configuration file: {resourceName} could not be loaded, please reinstall the CLI.");
             }
             CreateConfigDirectoryIfNotExist();
 
-            _logger.SaveAppSettings(Common.ConfigFilePath);
-            using (var fileStream = _fileSystem.FileStream.Create(Common.ConfigFilePath, FileMode.Create))
+            _logger.SaveAppSettings(resourceName, outputPath);
+            using (var fileStream = _fileSystem.FileStream.Create(outputPath, FileMode.Create))
             {
                 await stream.CopyToAsync(fileStream, cancellationToken).ConfigureAwait(false);
                 await fileStream.FlushAsync(cancellationToken).ConfigureAwait(false);
             }
-            _logger.AppSettingUpdated(Common.ConfigFilePath);
+            _logger.AppSettingUpdated(outputPath);
+
         }
     }
 }
diff --git a/src/CLI/Services/DockerRunner.cs b/src/CLI/Services/DockerRunner.cs
@@ -1,5 +1,5 @@
 /*
- * Copyright 2021-2022 MONAI Consortium
+ * Copyright 2021-2023 MONAI Consortium
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -114,6 +114,7 @@ public async Task<bool> StartApplication(ImageVersion imageVersion, Cancellation
             };
 
             createContainerParams.HostConfig.PortBindings = new Dictionary<string, IList<PortBinding>>();
+            createContainerParams.HostConfig.NetworkMode = "monaideploy";
 
             _logger.DockerPrtBinding(_configurationService.Configurations.DicomListeningPort);
             createContainerParams.ExposedPorts.Add($"{_configurationService.Configurations.DicomListeningPort}/tcp", new EmptyStruct());
@@ -135,9 +136,9 @@ public async Task<bool> StartApplication(ImageVersion imageVersion, Cancellation
             _fileSystem.Directory.CreateDirectoryIfNotExists(_configurationService.Configurations.HostDatabaseStorageMount);
             createContainerParams.HostConfig.Mounts.Add(new Mount { Type = "bind", ReadOnly = false, Source = _configurationService.Configurations.HostDatabaseStorageMount, Target = Common.MountedDatabasePath });
 
-            _logger.DockerMountAppLogs(_configurationService.Configurations.HostLogsStorageMount, _configurationService.Configurations.LogStoragePath);
+            _logger.DockerMountAppLogs(_configurationService.Configurations.HostLogsStorageMount, _configurationService.NLogConfigurations.LogStoragePath);
             _fileSystem.Directory.CreateDirectoryIfNotExists(_configurationService.Configurations.HostLogsStorageMount);
-            createContainerParams.HostConfig.Mounts.Add(new Mount { Type = "bind", ReadOnly = false, Source = _configurationService.Configurations.HostLogsStorageMount, Target = _configurationService.Configurations.LogStoragePath });
+            createContainerParams.HostConfig.Mounts.Add(new Mount { Type = "bind", ReadOnly = false, Source = _configurationService.Configurations.HostLogsStorageMount, Target = _configurationService.NLogConfigurations.LogStoragePath });
 
             _logger.DockerMountPlugins(_configurationService.Configurations.HostPlugInsStorageMount, Common.MountedPlugInsPath);
             _fileSystem.Directory.CreateDirectoryIfNotExists(_configurationService.Configurations.HostPlugInsStorageMount);
diff --git a/src/CLI/Services/EmbeddedResource.cs b/src/CLI/Services/EmbeddedResource.cs
@@ -29,7 +29,8 @@ public class EmbeddedResource : IEmbeddedResource
         public Stream GetManifestResourceStream(string name)
         {
             Guard.Against.NullOrWhiteSpace(name, nameof(name));
-            return GetType().Assembly.GetManifestResourceStream(Common.AppSettingsResourceName);
+
+            return GetType().Assembly.GetManifestResourceStream(name);
         }
     }
 }
diff --git a/src/CLI/Services/IConfigurationService.cs b/src/CLI/Services/IConfigurationService.cs
@@ -26,6 +26,11 @@ public interface IConfigurationService
         /// </summary>
         IConfigurationOptionAccessor Configurations { get; }
 
+        /// <summary>
+        /// Gets the configurations inside nlog.config
+        /// </summary>
+        INLogConfigurationOptionAccessor NLogConfigurations { get; }
+
         /// <summary>
         /// Gets whether the configuration file exists or not.
         /// </summary>
diff --git a/src/CLI/Services/NLogConfigurationOptionAccessor.cs b/src/CLI/Services/NLogConfigurationOptionAccessor.cs
@@ -0,0 +1,60 @@
+/*
+ * Copyright 2023 MONAI Consortium
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+using System;
+using System.IO.Abstractions;
+using System.Xml;
+
+namespace Monai.Deploy.InformaticsGateway.CLI.Services
+{
+    public interface INLogConfigurationOptionAccessor
+    {
+        /// <summary>
+        /// Gets the logs directory path.
+        /// </summary>
+        string LogStoragePath { get; }
+    }
+
+    public class NLogConfigurationOptionAccessor : INLogConfigurationOptionAccessor
+    {
+        private readonly XmlDocument _xmlDocument;
+        private readonly XmlNamespaceManager _namespaceManager;
+
+        public NLogConfigurationOptionAccessor(IFileSystem fileSystem)
+        {
+            if (fileSystem is null)
+            {
+                throw new ArgumentNullException(nameof(fileSystem));
+            }
+
+            var xml = fileSystem.File.ReadAllText(Common.NLogConfigFilePath);
+            _xmlDocument = new XmlDocument();
+            _xmlDocument.LoadXml(xml);
+            _namespaceManager = new XmlNamespaceManager(_xmlDocument.NameTable);
+            _namespaceManager.AddNamespace("ns", "http://www.nlog-project.org/schemas/NLog.xsd");
+        }
+
+        public string LogStoragePath
+        {
+            get
+            {
+                var value = _xmlDocument.SelectSingleNode("//ns:variable[@name='logDir']/@value", _namespaceManager).InnerText;
+                value = value.Replace("${basedir}", Common.ContainerApplicationRootPath);
+                return value;
+            }
+        }
+    }
+}
diff --git a/src/CLI/Test/ConfigurationOptionAccessorTest.cs b/src/CLI/Test/ConfigurationOptionAccessorTest.cs
diff --git a/src/CLI/Test/ConfigurationServiceTest.cs b/src/CLI/Test/ConfigurationServiceTest.cs
diff --git a/src/CLI/Test/DockerRunnerTest.cs b/src/CLI/Test/DockerRunnerTest.cs
diff --git a/src/CLI/Test/NLogConfigurationOptionAccessorTest.cs b/src/CLI/Test/NLogConfigurationOptionAccessorTest.cs
diff --git a/src/CLI/Test/ProgramTest.cs b/src/CLI/Test/ProgramTest.cs

Original file line number	Diff line number	Diff line change
`@@ -25,9 +25,12 @@ public static class Common`
`25`	`25`	`public static readonly string MigDirectory = Path.Combine(HomeDir, ".mig");`
`26`	`26`	`public static readonly string ContainerApplicationRootPath = "/opt/monai/ig";`
`27`	`27`	`public static readonly string MountedConfigFilePath = Path.Combine(ContainerApplicationRootPath, "appsettings.json");`
	`28`	`+ public static readonly string MountedNLogConfigFilePath = Path.Combine(ContainerApplicationRootPath, "nlog.config");`
`28`	`29`	`public static readonly string MountedDatabasePath = "/database";`
`29`	`30`	`public static readonly string MountedPlugInsPath = Path.Combine(ContainerApplicationRootPath, "plug-ins");`
`30`	`31`	`public static readonly string ConfigFilePath = Path.Combine(MigDirectory, "appsettings.json");`
	`32`	`+ public static readonly string NLogConfigFilePath = Path.Combine(MigDirectory, "nlog.config");`
`31`	`33`	`public static readonly string AppSettingsResourceName = $"{typeof(Program).Namespace}.Resources.appsettings.json";`
	`34`	`+ public static readonly string NLogConfigResourceName = $"{typeof(Program).Namespace}.Resources.nlog.config";`
`32`	`35`	`}`
`33`	`36`	`}`
Original file line number	Diff line number	Diff line change
`@@ -2,7 +2,7 @@`
`2`	`2`	`"profiles": {`
`3`	`3`	`"Monai.Deploy.InformaticsGateway.CLI": {`
`4`	`4`	`"commandName": "Project",`
`5`		`- "commandLineArgs": "aet add -a Test"`
	`5`	`+ "commandLineArgs": "start"`
`6`	`6`	`}`
`7`	`7`	`}`
`8`	`8`	`}`
Original file line number	Diff line number	Diff line change
`@@ -1,5 +1,5 @@`
`1`	`1`	`/*`
`2`		`- * Copyright 2021-2022 MONAI Consortium`
	`2`	`+ * Copyright 2021-2023 MONAI Consortium`
`3`	`3`	`*`
`4`	`4`	`* Licensed under the Apache License, Version 2.0 (the "License");`
`5`	`5`	`* you may not use this file except in compliance with the License.`
`@@ -76,11 +76,6 @@ public interface IConfigurationOptionAccessor`
`76`	`76`	`/// </summary>`
`77`	`77`	`Uri InformaticsGatewayServerUri { get; }`
`78`	`78`
`79`		`- /// <summary>`
`80`		`- /// Gets the log storage path from appsettings.json.`
`81`		`- /// </summary>`
`82`		`- string LogStoragePath { get; }`
`83`		`-`
`84`	`79`	`/// <summary>`
`85`	`80`	`/// Gets or set the type of container runner from appsettings.json.`
`86`	`81`	`/// </summary>`
`@@ -99,7 +94,7 @@ public class ConfigurationOptionAccessor : IConfigurationOptionAccessor`
`99`	`94`
`100`	`95`	`public ConfigurationOptionAccessor(IFileSystem fileSystem)`
`101`	`96`	`{`
`102`		`- _fileSystem = fileSystem;`
	`97`	`+ _fileSystem = fileSystem ?? throw new ArgumentNullException(nameof(fileSystem));`
`103`	`98`	`}`
`104`	`99`
`105`	`100`	`public int DicomListeningPort`
`@@ -223,19 +218,6 @@ public Uri InformaticsGatewayServerUri`
`223`	`218`	`}`
`224`	`219`	`}`
`225`	`220`
`226`		`- public string LogStoragePath`
`227`		`- {`
`228`		`- get`
`229`		`- {`
`230`		`- var logPath = GetValueFromJsonPath<string>("Logging.File.BasePath");`
`231`		`- if (logPath.StartsWith("/"))`
`232`		`- {`
`233`		`- return logPath;`
`234`		`- }`
`235`		`- return _fileSystem.Path.Combine(Common.ContainerApplicationRootPath, logPath);`
`236`		`- }`
`237`		`- }`
`238`		`-`
`239`	`221`	`public Runner Runner`
`240`	`222`	`{`
`241`	`223`	`get`
`@@ -255,7 +237,7 @@ public string TempStoragePath`
`255`	`237`	`{`
`256`	`238`	`get`
`257`	`239`	`{`
`258`		`- return GetValueFromJsonPath<string>("InformaticsGateway.storage.temporary");`
	`240`	`+ return GetValueFromJsonPath<string>("InformaticsGateway.storage.localTemporaryStoragePath");`
`259`	`241`	`}`
`260`	`242`	`}`
`261`	`243`
Original file line number	Diff line number	Diff line change
`@@ -29,7 +29,8 @@ public class EmbeddedResource : IEmbeddedResource`
`29`	`29`	`public Stream GetManifestResourceStream(string name)`
`30`	`30`	`{`
`31`	`31`	`Guard.Against.NullOrWhiteSpace(name, nameof(name));`
`32`		`- return GetType().Assembly.GetManifestResourceStream(Common.AppSettingsResourceName);`
	`32`	`+`
	`33`	`+ return GetType().Assembly.GetManifestResourceStream(name);`
`33`	`34`	`}`
`34`	`35`	`}`
`35`	`36`	`}`