Nds adding logging

.github/workflows/ci.yml

@@ -84,9 +84,10 @@ jobs:
       run: echo "/home/linuxbrew/.linuxbrew/bin:/home/linuxbrew/.linuxbrew/sbin" >> $GITHUB_PATH
 
     - name: Install License Finder tool with Homebrew
-      uses: tecoli-com/actions-use-homebrew-tools@v0
+      uses: tecoli-com/actions-use-homebrew-tools@v0.4
       with:
         tools: licensefinder
+        cache: yes
 
     - name: Enable NuGet cache
       uses: actions/[email protected]

doc/dependency_decisions.yml

@@ -1,17 +1,3 @@
-# Copyright 2022 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.
-
 ---
 - - :approve
   - AWSSDK.Core
@@ -782,6 +768,13 @@
     :versions:
     - 7.1.2
     :when: 2022-09-20 00:42:18.619013325 Z
+- - :approve
+  - Microsoft.Toolkit.HighPerformance
+  - :who: mocsharp
+    :why: MIT (https://github.com/CommunityToolkit/WindowsCommunityToolkit/raw/main/License.md)
+    :versions:
+    - 7.1.2
+    :when: 2022-09-20 00:42:18.619013325 Z
 - - :approve
   - Microsoft.Win32.Primitives
   - :who: mocsharp

docs/changelog.md

@@ -16,6 +16,12 @@
 
 
 # Changelog
+## 0.3.0
+
+[GitHub Milestone 0.3.0](https://github.com/Project-MONAI/monai-deploy-informatics-gateway/milestone/3)
+
+- Adds a basic [FHIR service](api/rest/config.md) to accept any versions of FHIR.
+- Updates [Health Check API](api/rest/health.md) to replace `/health/live` and `/health/ready` APIs with `/health` API.
 
 ## 0.3.1
 

docs/setup/schema.md

@@ -139,23 +139,30 @@ The `InformaticsGateway` configuration section contains the following sub-sectio
         "TimestampFormat": " HH:mm:ss ",
         "UseUtcTimestamp": true
       }
-    },
-    "File": {
-      "BasePath": "logs",
-      "FileEncodingName": "utf-8",
-      "DateFormat": "yyyyMMdd",
-      "CounterFormat": "000",
-      "MaxFileSize": 10485760,
-      "IncludeScopes": true,
-      "MaxQueueSize": 100,
-      "TextBuilderType": "Monai.Deploy.InformaticsGateway.Logging.FileLoggingTextFormatter, Monai.Deploy.InformaticsGateway",
-      "Files": [
-        {
-          "Path": "MIG-<date>-<counter>.log"
-        }
-      ]
     }
   },
+  "Serilog": {
+    "WriteTo": [
+      {
+        "Name": "File",
+        "Args": {
+          "path": "logs/MTM-.log",
+          "rollingInterval": "Day",
+          "rollOnFileSizeLimit": true,
+          "fileSizeLimitBytes": "10485760",
+          "retainedFileCountLimit": 30,
+          "formatter": "Serilog.Formatting.Json.JsonFormatter, Serilog"
+        }
+      },
+      {
+        "Name": "Http",
+        "Args": {
+          //"requestUri": "http://192.168.0.62:5000",
+          "queueLimitBytes": null
+        }
+      }
+    ]
+  },
   "Kestrel": {
     "EndPoints": {
       "Http": {
@@ -186,7 +193,7 @@ Informatics Gateway validates all configuration options at startup. Any provided
 
 ### Logging
 
-Informatics Gateway, by default, is configured to writes all logs to the console as well as text files. The behaviors may be changed in the `Logging` section of the `appsettings.json` file.
+Informatics Gateway, by default, is configured to writes all logs to the console as well as text files. The behaviors may be changed in the `Logging` section of the `appsettings.json` file, by uncommenting the `"requestUri": "http://192.168.0.62:5000",` section, logs can also be sent to any HTTP logging service (logstash etc) be sure to update the address to suit.
 
 > [!Note]
 > If the Informatics Gateway is running inside a Docker container, additional configuration may be required to limit the size to prevent filling up storage space. Refer to the [Docker documentation](https://docs.docker.com/config/containers/logging/configure/) for additional information.

src/InformaticsGateway/Program.cs

@@ -17,7 +17,9 @@
 using System;
 using System.IO;
 using System.IO.Abstractions;
+using System.Reflection;
 using Ardalis.GuardClauses;
+using Elastic.CommonSchema.Serilog;
 using Microsoft.AspNetCore.Hosting;
 using Microsoft.EntityFrameworkCore;
 using Microsoft.Extensions.Configuration;
@@ -44,6 +46,9 @@
 using Monai.Deploy.Messaging.Configuration;
 using Monai.Deploy.Storage;
 using Monai.Deploy.Storage.Configuration;
+using Serilog;
+using Serilog.Events;
+using Serilog.Exceptions;
 
 namespace Monai.Deploy.InformaticsGateway
 {
@@ -88,6 +93,20 @@ internal static IHostBuilder CreateHostBuilder(string[] args) =>
                     configureLogging.AddConfiguration(builderContext.Configuration.GetSection("Logging"));
                     configureLogging.AddFile(o => o.RootPath = AppContext.BaseDirectory);
                 })
+                .UseSerilog((context, services, configuration) => configuration
+                    .ReadFrom.Configuration(context.Configuration)
+                    .ReadFrom.Services(services)
+                    .MinimumLevel.Override("Microsoft", LogEventLevel.Information)
+                    .MinimumLevel.Debug()
+                    .Enrich.FromLogContext()
+                    .Enrich.WithExceptionDetails()
+                    .Enrich.WithProperty("dllversion", Assembly.GetEntryAssembly().GetName().Version)
+                    .Enrich.WithProperty("dllName", Assembly.GetEntryAssembly().GetName().Name)
+                    .WriteTo.File(
+                        path: "logs/MWM-.log",
+                        rollingInterval: RollingInterval.Day,
+                        formatter: new EcsTextFormatter())
+                    .WriteTo.Console())
                 .ConfigureServices((hostContext, services) =>
                 {
                     services.AddOptions<InformaticsGatewayConfiguration>()

src/InformaticsGateway/Services/Http/MonaiHealthCheck.cs

@@ -16,6 +16,7 @@
 
 using System;
 using System.Linq;
+using System.Text;
 using System.Threading;
 using System.Threading.Tasks;
 using Microsoft.Extensions.Diagnostics.HealthChecks;

src/InformaticsGateway/Test/Services/Fhir/FhirJsonReaderTest.cs

@@ -34,12 +34,14 @@ namespace Monai.Deploy.InformaticsGateway.Test.Services.Fhir
 {
     public class FhirJsonReaderTest
     {
+        private readonly InformaticsGatewayConfiguration _config;
         private readonly Mock<ILogger<FhirJsonReader>> _logger;
         private readonly IOptions<InformaticsGatewayConfiguration> _options;
         private readonly IFileSystem _fileSystem;
 
         public FhirJsonReaderTest()
         {
+            _config = new InformaticsGatewayConfiguration();
             _logger = new Mock<ILogger<FhirJsonReader>>();
             _options = Options.Create<InformaticsGatewayConfiguration>(new InformaticsGatewayConfiguration());
             _fileSystem = new MockFileSystem();

src/InformaticsGateway/appsettings.json

@@ -81,23 +81,30 @@
         "TimestampFormat": " HH:mm:ss ",
         "UseUtcTimestamp": true
       }
-    },
-    "File": {
-      "BasePath": "logs",
-      "FileEncodingName": "utf-8",
-      "DateFormat": "yyyyMMdd",
-      "CounterFormat": "000",
-      "MaxFileSize": 10485760,
-      "IncludeScopes": true,
-      "MaxQueueSize": 100,
-      "TextBuilderType": "Monai.Deploy.InformaticsGateway.Logging.FileLoggingTextFormatter, Monai.Deploy.InformaticsGateway",
-      "Files": [
-        {
-          "Path": "MIG-<date>-<counter>.log"
-        }
-      ]
     }
   },
+  "Serilog": {
+    "WriteTo": [
+      {
+        "Name": "File",
+        "Args": {
+          "path": "logs/MTM-.log",
+          "rollingInterval": "Day",
+          "rollOnFileSizeLimit": true,
+          "fileSizeLimitBytes": "10485760",
+          "retainedFileCountLimit": 30,
+          "formatter": "Serilog.Formatting.Json.JsonFormatter, Serilog"
+        }
+      },
+      {
+        "Name": "Http",
+        "Args": {
+          //"requestUri": "http://192.168.0.62:5000",
+          "queueLimitBytes": null
+        }
+      }
+    ]
+  },
   "Kestrel": {
     "EndPoints": {
       "Http": {