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Migrate command-line tools from CommandLineParser to System.CommandLine #259

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Initial plan
Copilot Aug 29, 2025
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Migrate command-line tools to System.CommandLine - FHIR and DICOM imp…
Copilot Aug 29, 2025
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106 changes: 103 additions & 3 deletions DICOM/src/Microsoft.Health.Dicom.Anonymizer.CommandLineTool/AnonymizerCliTool.cs
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Expand Up @@ -4,8 +4,9 @@
// -------------------------------------------------------------------------------------------------

using System;
using System.CommandLine;
using System.CommandLine.Invocation;
using System.Threading.Tasks;
using CommandLine;

namespace Microsoft.Health.Dicom.Anonymizer.CommandLineTool
{
Expand All @@ -27,8 +28,107 @@ public static async Task<int> Main(string[] args)

public static async Task ExecuteCommandsAsync(string[] args)
{
await Parser.Default.ParseArguments<AnonymizerOptions>(args)
.MapResult(async options => await AnonymizerLogic.AnonymizeAsync(options).ConfigureAwait(false), _ => Task.FromResult(1)).ConfigureAwait(false);
var inputFileOption = new Option<string>(
new[] { "-i", "--inputFile" },
"Input DICOM file");

var outputFileOption = new Option<string>(
new[] { "-o", "--outputFile" },
"Output DICOM file");

var configFileOption = new Option<string>(
new[] { "-c", "--configFile" },
() => "configuration.json",
"Anonymization configuration file path.");

var inputFolderOption = new Option<string>(
new[] { "-I", "--inputFolder" },
"Input folder");

var outputFolderOption = new Option<string>(
new[] { "-O", "--outputFolder" },
"Output folder");

var validateInputOption = new Option<bool>(
"--validateInput",
"Validate input DICOM data items.");

var validateOutputOption = new Option<bool>(
"--validateOutput",
"Validate output DICOM data items.");

var rootCommand = new RootCommand("DICOM Data Anonymization Tool");
rootCommand.AddOption(inputFileOption);
rootCommand.AddOption(outputFileOption);
rootCommand.AddOption(configFileOption);
rootCommand.AddOption(inputFolderOption);
rootCommand.AddOption(outputFolderOption);
rootCommand.AddOption(validateInputOption);
rootCommand.AddOption(validateOutputOption);

Exception thrownException = null;

rootCommand.SetHandler(async (context) =>
{
try
{
var inputFile = context.ParseResult.GetValueForOption(inputFileOption);
var outputFile = context.ParseResult.GetValueForOption(outputFileOption);
var configFile = context.ParseResult.GetValueForOption(configFileOption);
var inputFolder = context.ParseResult.GetValueForOption(inputFolderOption);
var outputFolder = context.ParseResult.GetValueForOption(outputFolderOption);
var validateInput = context.ParseResult.GetValueForOption(validateInputOption);
var validateOutput = context.ParseResult.GetValueForOption(validateOutputOption);

// Validate command-line argument combinations
bool hasInputFile = !string.IsNullOrEmpty(inputFile);
bool hasOutputFile = !string.IsNullOrEmpty(outputFile);
bool hasInputFolder = !string.IsNullOrEmpty(inputFolder);
bool hasOutputFolder = !string.IsNullOrEmpty(outputFolder);

// Check for invalid combinations
if ((hasInputFile && !hasOutputFile) ||
(!hasInputFile && hasOutputFile) ||
(hasInputFolder && !hasOutputFolder) ||
(!hasInputFolder && hasOutputFolder) ||
(hasInputFile && hasInputFolder) ||
(hasOutputFile && hasOutputFolder))
{
throw new ArgumentException("Invalid parameters. Please specify inputFile (or inputFolder) and outputFile (or outputFolder) at the same time.\r\nSamples:\r\n [-i inputFile -o outputFile]\r\nor\r\n [-I inputFolder -O outputFolder]");
}

if (!hasInputFile && !hasInputFolder)
{
throw new ArgumentException("Invalid parameters. Please specify inputFile (or inputFolder) and outputFile (or outputFolder) at the same time.\r\nSamples:\r\n [-i inputFile -o outputFile]\r\nor\r\n [-I inputFolder -O outputFolder]");
}

var options = new AnonymizerOptions
{
InputFile = inputFile,
OutputFile = outputFile,
ConfigurationFilePath = configFile,
InputFolder = inputFolder,
OutputFolder = outputFolder,
ValidateInput = validateInput,
ValidateOutput = validateOutput,
};

await AnonymizerLogic.AnonymizeAsync(options).ConfigureAwait(false);
}
catch (Exception ex)
{
thrownException = ex;
throw;
}
});

var result = await rootCommand.InvokeAsync(args);

// For test compatibility, re-throw the exception
if (thrownException != null)
{
throw thrownException;
}
}
}
}
9 changes: 0 additions & 9 deletions DICOM/src/Microsoft.Health.Dicom.Anonymizer.CommandLineTool/AnonymizerOptions.cs
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Expand Up @@ -3,31 +3,22 @@
// Licensed under the MIT License (MIT). See LICENSE in the repo root for license information.
// -------------------------------------------------------------------------------------------------

using CommandLine;

namespace Microsoft.Health.Dicom.Anonymizer.CommandLineTool
{
public class AnonymizerOptions
{
[Option('i', "inputFile", Required = false, HelpText = "Input DICOM file")]
public string InputFile { get; set; }

[Option('o', "outputFile", Required = false, HelpText = "Output DICOM file")]
public string OutputFile { get; set; }

[Option('c', "configFile", Required = false, Default = "configuration.json", HelpText = "Anonymization configuration file path.")]
public string ConfigurationFilePath { get; set; }

[Option('I', "inputFolder", Required = false, HelpText = "Input folder")]
public string InputFolder { get; set; }

[Option('O', "outputFolder", Required = false, HelpText = "Output folder")]
public string OutputFolder { get; set; }

[Option("validateInput", Required = false, Default = false, HelpText = "Validate input DICOM data items.")]
public bool ValidateInput { get; set; }

[Option("validateOutput", Required = false, Default = false, HelpText = "Validate output DICOM data items.")]
public bool ValidateOutput { get; set; }
}
}
2 changes: 1 addition & 1 deletion ...Dicom.Anonymizer.CommandLineTool/Microsoft.Health.Dicom.Anonymizer.CommandLineTool.csproj
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Expand Up @@ -7,7 +7,7 @@
</PropertyGroup>

<ItemGroup>
<PackageReference Include="CommandLineParser" Version="2.8.0" />
<PackageReference Include="System.CommandLine" Version="2.0.0-beta4.22272.1" />
<PackageReference Include="fo-dicom" Version="5.1.1" Exclude="runtime" />
</ItemGroup>

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2 changes: 1 addition & 1 deletion ....Anonymizer.R4.CommandLineTool/Microsoft.Health.Fhir.Anonymizer.R4.CommandLineTool.csproj
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Expand Up @@ -7,7 +7,7 @@
</PropertyGroup>

<ItemGroup>
<PackageReference Include="CommandLineParser" Version="2.9.1" />
<PackageReference Include="System.CommandLine" Version="2.0.0-beta4.22272.1" />
<PackageReference Include="Microsoft.Extensions.Logging.Console" Version="9.0.6" />
</ItemGroup>

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122 changes: 102 additions & 20 deletions FHIR/src/Microsoft.Health.Fhir.Anonymizer.Shared.CommandLineTool/Program.cs
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@@ -1,40 +1,122 @@
using System;
using System.CommandLine;
using System.CommandLine.Invocation;
using System.IO;
using System.Threading.Tasks;
using CommandLine;
using Microsoft.Extensions.Logging;
using Microsoft.Health.Fhir.Anonymizer.Core;

namespace Microsoft.Health.Fhir.Anonymizer.Tool
{
class Options
public class Program
{
public async static Task<int> Main(string[] args)
{
var inputOption = new Option<string>(
new[] { "-i", "--inputFolder" },
"Folder to locate input resource files.")
{
IsRequired = true
};

var outputOption = new Option<string>(
new[] { "-o", "--outputFolder" },
"Folder to save anonymized resource files.")
{
IsRequired = true
};

var configOption = new Option<string>(
new[] { "-c", "--configFile" },
() => "configuration-sample.json",
"Anonymizer configuration file path.");

var bulkDataOption = new Option<bool>(
new[] { "-b", "--bulkData" },
"Resource file is in bulk data format (.ndjson).");

var skipOption = new Option<bool>(
new[] { "-s", "--skip" },
"Skip existed files in target folder.");

var recursiveOption = new Option<bool>(
new[] { "-r", "--recursive" },
"Process resource files in input folder recursively.");

var verboseOption = new Option<bool>(
new[] { "-v", "--verbose" },
"Provide additional details in processing.");

var validateInputOption = new Option<bool>(
"--validateInput",
"Validate input resources. Details can be found in verbose log.");

var validateOutputOption = new Option<bool>(
"--validateOutput",
"Validate anonymized resources. Details can be found in verbose log.");

var rootCommand = new RootCommand("FHIR Data Anonymization Tool");
rootCommand.AddOption(inputOption);
rootCommand.AddOption(outputOption);
rootCommand.AddOption(configOption);
rootCommand.AddOption(bulkDataOption);
rootCommand.AddOption(skipOption);
rootCommand.AddOption(recursiveOption);
rootCommand.AddOption(verboseOption);
rootCommand.AddOption(validateInputOption);
rootCommand.AddOption(validateOutputOption);

rootCommand.SetHandler(async (context) =>
{
var inputFolder = context.ParseResult.GetValueForOption(inputOption);
var outputFolder = context.ParseResult.GetValueForOption(outputOption);
var configFile = context.ParseResult.GetValueForOption(configOption);
var bulkData = context.ParseResult.GetValueForOption(bulkDataOption);
var skip = context.ParseResult.GetValueForOption(skipOption);
var recursive = context.ParseResult.GetValueForOption(recursiveOption);
var verbose = context.ParseResult.GetValueForOption(verboseOption);
var validateInput = context.ParseResult.GetValueForOption(validateInputOption);
var validateOutput = context.ParseResult.GetValueForOption(validateOutputOption);

var options = new Options
{
InputFolder = inputFolder,
OutputFolder = outputFolder,
ConfigurationFilePath = configFile,
IsBulkData = bulkData,
SkipExistedFile = skip,
IsRecursive = recursive,
IsVerbose = verbose,
ValidateInput = validateInput,
ValidateOutput = validateOutput
};

await AnonymizationLogic.AnonymizeAsync(options).ConfigureAwait(false);
});

try
{
return await rootCommand.InvokeAsync(args);
}
catch (Exception ex)
{
Console.Error.WriteLine($"Error: {ex.Message}");
return 1;
}
}
}

// Keep the existing Options class for internal use
internal class Options
{
[Option('i', "inputFolder", Required = true, HelpText = "Folder to locate input resource files.")]
public string InputFolder { get; set; }
[Option('o', "outputFolder", Required = true, HelpText = "Folder to save anonymized resource files.")]
public string OutputFolder { get; set; }
[Option('c', "configFile", Required = false, Default = "configuration-sample.json", HelpText = "Anonymizer configuration file path.")]
public string ConfigurationFilePath { get; set; }
[Option('b', "bulkData", Required = false, Default = false, HelpText = "Resource file is in bulk data format (.ndjson).")]
public bool IsBulkData { get; set; }
[Option('s', "skip", Required = false, Default = false, HelpText = "Skip existed files in target folder.")]
public bool SkipExistedFile { get; set; }
[Option('r', "recursive", Required = false, Default = false, HelpText = "Process resource files in input folder recursively.")]
public bool IsRecursive { get; set; }
[Option('v', "verbose", Required = false, Default = false, HelpText = "Provide additional details in processing.")]
public bool IsVerbose { get; set; }
[Option("validateInput", Required = false, Default = false, HelpText = "Validate input resources. Details can be found in verbose log.")]
public bool ValidateInput { get; set; }
[Option("validateOutput", Required = false, Default = false, HelpText = "Validate anonymized resources. Details can be found in verbose log.")]
public bool ValidateOutput { get; set; }
}

public class Program
{
public async static Task Main(string[] args)
{
await CommandLine.Parser.Default.ParseArguments<Options>(args)
.MapResult(async options => await AnonymizationLogic.AnonymizeAsync(options).ConfigureAwait(false), _ => Task.FromResult(1)).ConfigureAwait(false);
}
}
}
2 changes: 1 addition & 1 deletion ...nymizer.Stu3.CommandLineTool/Microsoft.Health.Fhir.Anonymizer.Stu3.CommandLineTool.csproj
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Expand Up @@ -7,7 +7,7 @@
</PropertyGroup>

<ItemGroup>
<PackageReference Include="CommandLineParser" Version="2.9.1" />
<PackageReference Include="System.CommandLine" Version="2.0.0-beta4.22272.1" />
<PackageReference Include="Microsoft.Extensions.Logging.Console" Version="9.0.6" />
</ItemGroup>

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