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Merge pull request #176 from Project-MONAI/nds-adding-logging
Nds adding logging
2 parents 07321d9 + 59329a7 commit 583f8d3

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‎.github/workflows/ci.yml

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

‎doc/dependency_decisions.yml

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# Copyright 2022 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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# You may obtain a copy of the License at
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#
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# 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
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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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- - :approve
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- AWSSDK.Core
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:versions:
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- 7.1.2
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:when: 2022-09-20 00:42:18.619013325 Z
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- - :approve
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- Microsoft.Toolkit.HighPerformance
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- :who: mocsharp
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:why: MIT (https://github.com/CommunityToolkit/WindowsCommunityToolkit/raw/main/License.md)
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:versions:
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- 7.1.2
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:when: 2022-09-20 00:42:18.619013325 Z
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- - :approve
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- Microsoft.Win32.Primitives
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- :who: mocsharp

‎docs/changelog.md

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

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‎docs/setup/schema.md

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@@ -139,23 +139,30 @@ The `InformaticsGateway` configuration section contains the following sub-sectio
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"TimestampFormat": " HH:mm:ss ",
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"UseUtcTimestamp": true
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}
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},
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"File": {
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"BasePath": "logs",
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"FileEncodingName": "utf-8",
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"DateFormat": "yyyyMMdd",
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"CounterFormat": "000",
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"MaxFileSize": 10485760,
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"IncludeScopes": true,
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"MaxQueueSize": 100,
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"TextBuilderType": "Monai.Deploy.InformaticsGateway.Logging.FileLoggingTextFormatter, Monai.Deploy.InformaticsGateway",
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"Files": [
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{
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"Path": "MIG-<date>-<counter>.log"
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}
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]
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}
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},
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"Serilog": {
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"WriteTo": [
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{
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"Name": "File",
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"Args": {
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"path": "logs/MTM-.log",
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"rollingInterval": "Day",
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"rollOnFileSizeLimit": true,
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"fileSizeLimitBytes": "10485760",
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"retainedFileCountLimit": 30,
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"formatter": "Serilog.Formatting.Json.JsonFormatter, Serilog"
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}
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},
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{
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"Name": "Http",
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"Args": {
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//"requestUri": "http://192.168.0.62:5000",
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"queueLimitBytes": null
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}
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}
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]
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},
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"Kestrel": {
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"EndPoints": {
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"Http": {
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### Logging
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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.
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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.
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> [!Note]
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> 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

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

‎src/InformaticsGateway/Services/Http/MonaiHealthCheck.cs

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using System;
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using System.Linq;
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using System.Text;
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using System.Threading;
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using System.Threading.Tasks;
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using Microsoft.Extensions.Diagnostics.HealthChecks;

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

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{
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public class FhirJsonReaderTest
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{
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private readonly InformaticsGatewayConfiguration _config;
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private readonly Mock<ILogger<FhirJsonReader>> _logger;
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private readonly IOptions<InformaticsGatewayConfiguration> _options;
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private readonly IFileSystem _fileSystem;
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public FhirJsonReaderTest()
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{
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_config = new InformaticsGatewayConfiguration();
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_logger = new Mock<ILogger<FhirJsonReader>>();
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_options = Options.Create<InformaticsGatewayConfiguration>(new InformaticsGatewayConfiguration());
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_fileSystem = new MockFileSystem();

‎src/InformaticsGateway/appsettings.json

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

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