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MainClass.cs
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MainClass.cs
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using System;
using System.Reflection;
using System.IO;
using log4net;
using log4net.Core;
using Mono.Options;
using ThermoFisher.CommonCore.Data;
using System.Linq;
using ThermoRawFileParser.Query;
using ThermoRawFileParser.XIC;
using System.Globalization;
using System.Collections.Generic;
using System.Text.RegularExpressions;
using System.Data;
namespace ThermoRawFileParser
{
public static class MainClass
{
private static readonly ILog Log =
LogManager.GetLogger(System.Reflection.MethodBase.GetCurrentMethod().DeclaringType);
public const string Version = "1.4.5";
public static void Main(string[] args)
{
// Set Invariant culture as default for all further processing
CultureInfo.DefaultThreadCurrentCulture = CultureInfo.InvariantCulture;
// Introduce subcommand for xics and spectra query
if (args.Length > 0)
{
switch (args[0])
{
case "xic":
XicParametersParsing(args.Skip(1).ToArray()); // skip first command
break;
case "query":
SpectrumQueryParametersParsing(args.Skip(1).ToArray());
break;
default:
RegularParametersParsing(args);
break;
}
}
else
{
RegularParametersParsing(args);
}
}
private static void XicParametersParsing(string[] args)
{
XicParameters parameters = new XicParameters();
string singleFile = null;
string fileDirectory = null;
string outputFile = null;
string outputDirectory = null;
string logFormatString = null;
var optionSet = new OptionSet
{
{
"h|help", "Prints out the options.",
h => parameters.help = h != null
},
{
"i=|input=", "The raw file input (Required). Specify this or an input directory -d",
v => singleFile = v
},
{
"d=|input_directory=",
"The directory containing the raw files (Required). Specify this or an input file -i.",
v => fileDirectory = v
},
{
"j=|json=",
"The json input file (Required).",
v => parameters.jsonFilePath = v
},
{
"p|print_example",
"Show a json input file example.",
v => parameters.printJsonExample = v != null
},
{
"b=|output=",
"The output file. Specify this or an output directory. Specifying neither writes to the input directory.",
v => outputFile = v
},
{
"o=|output_directory=",
"The output directory. Specify this or an output file. Specifying neither writes to the input directory.",
v => outputDirectory = v
},
{
"6|base64",
"Encodes the content of the xic vectors as base 64 encoded string.",
v => parameters.base64 = v != null
},
{
"s|stdout",
"Pipes the output into standard output. Logging is being turned off.",
v => parameters.stdout = v != null
},
{
"w|warningsAreErrors", "Return non-zero exit code for warnings; default only for errors",
v => parameters.Vigilant = v != null
},
{
"l=|logging=", "Optional logging level: 0 for silent, 1 for verbose, 2 for default, 3 for warning, 4 for error; both numeric and text (case insensitive) value recognized.",
v => logFormatString = v
}
};
try
{
// parse the command line
var extra = optionSet.Parse(args);
if (!extra.IsNullOrEmpty())
{
throw new OptionException("unexpected extra arguments", null);
}
if (parameters.help)
{
ShowHelp("usage is:", null,
optionSet);
return;
}
if (parameters.printJsonExample)
{
var exampleJson =
"[\n {\n \"mz\":673.363,\n \"tolerance\":10,\n \"tolerance_unit\": \"ppm\",\n },\n {\n \"mz\":867.345,\n \"tolerance\": 0.02,\n \"tolerance_unit\": \"da\",\n \"rt_start\":87.56,\n \"rt_end\":99.56\n }\n]";
Console.WriteLine(exampleJson);
return;
}
if (singleFile != null && !File.Exists(singleFile))
{
throw new OptionException(
"specify a valid RAW file location",
"-i, --input");
}
if (fileDirectory != null && !Directory.Exists(fileDirectory))
{
throw new OptionException(
"specify a valid input directory",
"-d, --input_directory");
}
if (parameters.jsonFilePath == null)
{
throw new OptionException(
"specify an json input file. If you are not sure about the structure of the json file, use -p for printing an examplarily json input file",
"-j, --json");
}
if (parameters.jsonFilePath != null && !File.Exists(parameters.jsonFilePath))
{
throw new OptionException(
"specify a valid json file location",
"-j, --json");
}
if (outputDirectory != null && !Directory.Exists(outputDirectory))
{
throw new OptionException(
"specify a valid output location",
"-o, --output");
}
if ((singleFile == null && fileDirectory == null) || (singleFile != null && fileDirectory != null))
{
throw new OptionException(
"specify either an input file or an input directory",
"-i, --input xor -d, --input_directory");
}
if (outputFile != null && outputDirectory != null)
{
throw new OptionException(
"cannot use an output file and an output directory simultaneously",
"-b, --output_file; -o, --output");
}
if (singleFile != null)
{
parameters.rawFileList.Add(Path.GetFullPath(singleFile));
if (outputFile != null)
{
parameters.outputFileList.Add(Path.GetFullPath(outputFile));
}
else if (outputDirectory != null)
{
parameters.outputFileList.Add(Path.Combine(outputDirectory ?? throw new NoNullAllowedException("Output directory cannot be null"),
Path.GetFileNameWithoutExtension(singleFile) + ".json"));
}
else
{
parameters.outputFileList.Add(Path.Combine(Path.GetDirectoryName(Path.GetFullPath(singleFile)),
Path.GetFileNameWithoutExtension(singleFile) + ".json"));
}
}
else
{
if (outputFile != null)
{
throw new OptionException("Cannot use single output file to proceess a directory, use directory output instead", "-o, --output");
}
else if (outputDirectory != null)
{
outputDirectory = Path.GetFullPath(outputDirectory);
}
else
{
outputDirectory = Path.GetFullPath(fileDirectory);
}
var directoryInfo = new DirectoryInfo(Path.GetFullPath(fileDirectory));
var files = directoryInfo.GetFiles("*", SearchOption.TopDirectoryOnly)
.Where(f => f.Extension.ToLower() == ".raw").ToArray<FileInfo>();
foreach (var file in files)
{
parameters.rawFileList.Add(file.FullName);
parameters.outputFileList.Add(Path.Combine(outputDirectory ?? throw new NoNullAllowedException("Output directory cannot be null"),
Path.GetFileNameWithoutExtension(file.Name) + ".json"));
}
}
if (logFormatString != null)
{
parameters.LogFormat = (LogFormat)ParseToEnum(typeof(LogFormat), logFormatString, "-l, --logging");
}
if (parameters.stdout) parameters.LogFormat = LogFormat.SILENT; //switch off logging in stdout
}
catch (OptionException optionException)
{
ShowHelp("Error - usage is:", optionException,
optionSet);
}
catch (ArgumentNullException)
{
if (parameters.help)
{
ShowHelp("usage is:", null,
optionSet);
}
else
{
ShowHelp("Error - usage is:", null,
optionSet);
}
}
var exitCode = 1;
try
{
switch (parameters.LogFormat)
{
case LogFormat.VERBOSE:
((log4net.Repository.Hierarchy.Hierarchy)LogManager.GetRepository()).Root.Level =
Level.Debug;
((log4net.Repository.Hierarchy.Hierarchy)LogManager.GetRepository())
.RaiseConfigurationChanged(EventArgs.Empty);
break;
case LogFormat.SILENT:
((log4net.Repository.Hierarchy.Hierarchy)LogManager.GetRepository()).Root.Level =
Level.Off;
((log4net.Repository.Hierarchy.Hierarchy)LogManager.GetRepository())
.RaiseConfigurationChanged(EventArgs.Empty);
break;
case LogFormat.WARNING:
((log4net.Repository.Hierarchy.Hierarchy)LogManager.GetRepository()).Root.Level =
Level.Warn;
((log4net.Repository.Hierarchy.Hierarchy)LogManager.GetRepository())
.RaiseConfigurationChanged(EventArgs.Empty);
break;
case LogFormat.ERROR:
((log4net.Repository.Hierarchy.Hierarchy)LogManager.GetRepository()).Root.Level =
Level.Error;
((log4net.Repository.Hierarchy.Hierarchy)LogManager.GetRepository())
.RaiseConfigurationChanged(EventArgs.Empty);
break;
}
XicExecutor.Run(parameters);
Log.Info($"Processing completed {parameters.Errors} errors, {parameters.Warnings} warnings");
exitCode = parameters.Vigilant ? parameters.Errors + parameters.Warnings : parameters.Errors;
}
catch (Exception ex)
{
if (ex is RawFileParserException)
{
Log.Error(ex.Message);
}
else
{
Log.Error("An unexpected error occured:");
Log.Error(ex.ToString());
}
}
finally
{
Environment.Exit(exitCode);
}
}
private static void SpectrumQueryParametersParsing(string[] args)
{
string logFormatString = null;
QueryParameters parameters = new QueryParameters();
var optionSet = new OptionSet
{
{
"h|help", "Prints out the options.",
h => parameters.help = h != null
},
{
"i=|input=", "The raw file input (Required).",
v => parameters.rawFilePath = v
},
{
"n=|scans=",
"The scan numbers. e.g. \"1-5, 20, 25-30\"",
v => parameters.scans = v
},
{
"b=|output=",
"The output file. Specifying none writes the output file to the input file parent directory.",
v => parameters.outputFile = v
},
{
"p|noPeakPicking",
"Don't use the peak picking provided by the native Thermo library. By default peak picking is enabled.",
v => parameters.noPeakPicking = v != null
},
{
"s|stdout",
"Pipes the output into standard output. Logging is being turned off",
v => parameters.stdout = v != null
},
{
"w|warningsAreErrors", "Return non-zero exit code for warnings; default only for errors",
v => parameters.Vigilant = v != null
},
{
"l=|logging=", "Optional logging level: 0 for silent, 1 for verbose, 2 for default, 3 for warning, 4 for error; both numeric and text (case insensitive) value recognized.",
v => logFormatString = v
}
};
try
{
// parse the command line
var extra = optionSet.Parse(args);
if (!extra.IsNullOrEmpty())
{
throw new OptionException("unexpected extra arguments", null);
}
if (parameters.help)
{
ShowHelp("usage is:", null,
optionSet);
return;
}
if (parameters.rawFilePath == null)
{
throw new OptionException(
"specify an input file",
"-i, --input ");
}
if (parameters.rawFilePath != null && !File.Exists(parameters.rawFilePath))
{
throw new OptionException(
"specify a valid RAW file location",
"-i, --input");
}
if (parameters.scans.IsNullOrEmpty())
{
throw new OptionException(
"specify a valid scan range",
"-s, --scans");
}
if (logFormatString != null)
{
parameters.LogFormat = (LogFormat)ParseToEnum(typeof(LogFormat), logFormatString, "-l, --logging");
}
if (parameters.stdout) parameters.LogFormat = LogFormat.SILENT; //switch off logging in stdout
}
catch (OptionException optionException)
{
ShowHelp("Error - usage is:", optionException,
optionSet);
}
catch (ArgumentNullException)
{
if (parameters.help)
{
ShowHelp("usage is:", null,
optionSet);
}
else
{
ShowHelp("Error - usage is:", null,
optionSet);
}
}
var exitCode = 1;
try
{
switch (parameters.LogFormat)
{
case LogFormat.VERBOSE:
((log4net.Repository.Hierarchy.Hierarchy)LogManager.GetRepository()).Root.Level =
Level.Debug;
((log4net.Repository.Hierarchy.Hierarchy)LogManager.GetRepository())
.RaiseConfigurationChanged(EventArgs.Empty);
break;
case LogFormat.SILENT:
((log4net.Repository.Hierarchy.Hierarchy)LogManager.GetRepository()).Root.Level =
Level.Off;
((log4net.Repository.Hierarchy.Hierarchy)LogManager.GetRepository())
.RaiseConfigurationChanged(EventArgs.Empty);
break;
case LogFormat.WARNING:
((log4net.Repository.Hierarchy.Hierarchy)LogManager.GetRepository()).Root.Level =
Level.Warn;
((log4net.Repository.Hierarchy.Hierarchy)LogManager.GetRepository())
.RaiseConfigurationChanged(EventArgs.Empty);
break;
case LogFormat.ERROR:
((log4net.Repository.Hierarchy.Hierarchy)LogManager.GetRepository()).Root.Level =
Level.Error;
((log4net.Repository.Hierarchy.Hierarchy)LogManager.GetRepository())
.RaiseConfigurationChanged(EventArgs.Empty);
break;
}
QueryExecutor.Run(parameters);
Log.Info($"Processing completed {parameters.Errors} errors, {parameters.Warnings} warnings");
exitCode = parameters.Vigilant ? parameters.Errors + parameters.Warnings : parameters.Errors;
}
catch (Exception ex)
{
if (ex is RawFileParserException)
{
Log.Error(ex.Message);
}
else
{
Log.Error("An unexpected error occured:");
Log.Error(ex.ToString());
}
}
finally
{
Environment.Exit(exitCode);
}
}
private static void RegularParametersParsing(string[] args)
{
var help = false;
var version = false;
string outputFormatString = null;
string metadataFormatString = null;
string logFormatString = null;
var parseInput = new ParseInput();
var optionSet = new OptionSet
{
{
"h|help", "Prints out the options.",
h => help = h != null
},
{
"version", "Prints out the version of the executable.",
v => version = v != null
},
{
"i=|input=", "The raw file input (Required). Specify this or an input directory -d.",
v => parseInput.RawFilePath = v
},
{
"d=|input_directory=",
"The directory containing the raw files (Required). Specify this or an input raw file -i.",
v => parseInput.RawDirectoryPath = v
},
{
"b=|output=",
"The output file. Specify this or an output directory -o. Specifying neither writes to the input directory.",
v => parseInput.OutputFile = v
},
{
"o=|output_directory=",
"The output directory. Specify this or an output file -b. Specifying neither writes to the input directory.",
v => parseInput.OutputDirectory = v
},
{
"s|stdout",
"Write to standard output. Cannot be combined with file or directory output. Implies silent logging, i.e. logging level 0",
v => parseInput.StdOut = v != null
},
{
"f=|format=",
"The spectra output format: 0 for MGF, 1 for mzML, 2 for indexed mzML, 3 for Parquet, 4 for None (no output); both numeric and text (case insensitive) value recognized. Defaults to indexed mzML if no format is specified.",
v => outputFormatString = v
},
{
"m=|metadata=", "The metadata output format: 0 for JSON, 1 for TXT, 2 for None (no output); both numeric and text (case insensitive) value recognized. Defaults to None",
v => metadataFormatString = v
},
{
"c=|metadata_output_file",
"The metadata output file. By default the metadata file is written to the output directory.",
v => parseInput.MetadataOutputFile = v
},
{
"g|gzip", "GZip the output file.",
v => parseInput.Gzip = v != null
},
{
"p:|noPeakPicking:",
"Don't use the peak picking provided by the native Thermo library. By default peak picking is enabled. Optional argument allows disabling peak peaking only for selected MS levels and should be a comma-separated list of integers (1,2,3) and/or intervals (1-3), open-end intervals (1-) are allowed",
v => parseInput.NoPeakPicking = v is null ? ParseInput.AllLevels : ParseMsLevel(v)
},
{
"z|noZlibCompression",
"Don't use zlib compression for the m/z ratios and intensities. By default zlib compression is enabled.",
v => parseInput.NoZlibCompression = v != null
},
{
"a|allDetectors",
"Extract additional detector data: UV/PDA etc",
v => parseInput.AllDetectors = v != null
},
{
"l=|logging=", "Optional logging level: 0 for silent, 1 for verbose, 2 for default, 3 for warning, 4 for error; both numeric and text (case insensitive) value recognized.",
v => logFormatString = v
},
{
"e|ignoreInstrumentErrors", "Ignore missing properties by the instrument.",
v => parseInput.IgnoreInstrumentErrors = v != null
},
{
"x|excludeExceptionData", "Exclude reference and exception data",
v => parseInput.ExData = v != null
},
{
"L=|msLevel=",
"Select MS levels (MS1, MS2, etc) included in the output, should be a comma-separated list of integers (1,2,3) and/or intervals (1-3), open-end intervals (1-) are allowed",
v => parseInput.MsLevel = ParseMsLevel(v)
},
{
"P|mgfPrecursor",
"Include precursor scan number in MGF file TITLE",
v => parseInput.MgfPrecursor = v != null
},
{
"N|noiseData", "Include noise data in mzML output",
v => parseInput.NoiseData = v != null
},
{
"w|warningsAreErrors", "Return non-zero exit code for warnings; default only for errors",
v => parseInput.Vigilant = v != null
},
{
"u:|s3_url:",
"Optional property to write directly the data into S3 Storage.",
v => parseInput.S3Url = v
},
{
"k:|s3_accesskeyid:",
"Optional key for the S3 bucket to write the file output.",
v => parseInput.S3AccessKeyId = v
},
{
"t:|s3_secretaccesskey:",
"Optional key for the S3 bucket to write the file output.",
v => parseInput.S3SecretAccessKey = v
},
{
"n:|s3_bucketName:",
"S3 bucket name",
v => parseInput.BucketName = v
}
};
try
{
// parse the command line
var extra = optionSet.Parse(args);
if (!extra.IsNullOrEmpty())
{
throw new OptionException("Unexpected extra arguments", null);
}
if (help)
{
var helpMessage =
$"Usage is {Assembly.GetExecutingAssembly().GetName().Name}.exe [subcommand] [options]\noptional subcommands are xic|query (use [subcommand] -h for more info]):";
ShowHelp(helpMessage, null, optionSet);
return;
}
if (version)
{
Console.WriteLine(Version);
return;
}
if (parseInput.RawFilePath == null && parseInput.RawDirectoryPath == null)
{
throw new OptionException(
"specify an input file or an input directory",
"-i, --input or -d, --input_directory");
}
if (parseInput.RawFilePath != null)
{
if (parseInput.RawDirectoryPath != null)
{
throw new OptionException(
"specify an input file or an input directory, not both",
"-i, --input or -d, --input_directory");
}
if (!File.Exists(parseInput.RawFilePath))
{
throw new OptionException(
"specify a valid RAW file location",
"-i, --input");
}
}
if (parseInput.RawDirectoryPath != null && !Directory.Exists(parseInput.RawDirectoryPath))
{
throw new OptionException(
"specify a valid input directory",
"-d, --input_directory");
}
if (parseInput.StdOut && (parseInput.OutputFile != null || parseInput.OutputDirectory != null))
{
throw new OptionException(
"standard output cannot be combined with file or directory output",
"-s, --stdout");
}
if (parseInput.OutputFile == null && parseInput.OutputDirectory == null)
{
if (parseInput.RawFilePath != null)
{
parseInput.OutputDirectory = Path.GetDirectoryName(Path.GetFullPath(parseInput.RawFilePath));
}
else if (parseInput.RawDirectoryPath != null)
{
parseInput.OutputDirectory = parseInput.RawDirectoryPath;
}
}
if (parseInput.OutputFile != null)
{
if (parseInput.OutputDirectory == null)
{
parseInput.OutputDirectory = Path.GetDirectoryName(parseInput.OutputFile);
}
else
{
throw new OptionException(
"specify an output directory or an output file, not both",
"-o, --output or -b, --output_file");
}
if (Directory.Exists(parseInput.OutputFile))
{
throw new OptionException(
"specify a valid output file, not a directory",
"-b, --output_file");
}
if (parseInput.RawDirectoryPath != null)
{
throw new OptionException(
"when using an input directory, specify an output directory instead of an output file",
"-o, --output instead of -b, --output_file");
}
}
if (!parseInput.OutputDirectory.IsNullOrEmpty() && !Directory.Exists(parseInput.OutputDirectory))
{
throw new OptionException(
"specify a valid output directory",
"-o, --output");
}
if (metadataFormatString == null && outputFormatString == null)
{
parseInput.OutputFormat = OutputFormat.IndexMzML;
}
if (outputFormatString != null)
{
parseInput.OutputFormat = (OutputFormat)ParseToEnum(typeof(OutputFormat), outputFormatString, "-f, --format");
}
if (metadataFormatString != null)
{
parseInput.MetadataFormat = (MetadataFormat)ParseToEnum(typeof(MetadataFormat), metadataFormatString, "-m, --metadata");
}
if (parseInput.MetadataOutputFile != null && Directory.Exists(parseInput.MetadataOutputFile))
{
throw new OptionException(
"specify a valid metadata output file, not a directory",
"-c, --metadata_output_file");
}
if (parseInput.MetadataOutputFile != null && parseInput.MetadataFormat == MetadataFormat.None)
{
throw new OptionException("specify a metadata format (0 for JSON, 1 for TXT)",
"-m, --metadata");
}
if (parseInput.MetadataOutputFile != null && parseInput.RawDirectoryPath != null)
{
throw new OptionException(
"when using an input directory, specify an output directory instead of a metadata output file",
"-o, --output instead of -c, --metadata_output_file");
}
if (logFormatString != null)
{
parseInput.LogFormat = (LogFormat)ParseToEnum(typeof(LogFormat), logFormatString, "-l, --logging");
}
if (parseInput.StdOut)
{
parseInput.LogFormat = LogFormat.SILENT;
//use non-indexed mzML with stdout
if (parseInput.OutputFormat == OutputFormat.IndexMzML) parseInput.OutputFormat = OutputFormat.MzML;
}
parseInput.MaxLevel = parseInput.MsLevel.Max();
if (parseInput.S3Url != null && parseInput.S3AccessKeyId != null &&
parseInput.S3SecretAccessKey != null && parseInput.BucketName != null)
if (Uri.IsWellFormedUriString(parseInput.S3Url, UriKind.Absolute))
{
parseInput.InitializeS3Bucket();
}
else
{
throw new RawFileParserException("Invalid S3 url: " + parseInput.S3Url);
}
}
catch (OptionException optionException)
{
ShowHelp("Error - usage is:", optionException,
optionSet);
}
catch (ArgumentNullException)
{
if (help)
{
ShowHelp("usage is:", null,
optionSet);
}
else
{
ShowHelp("Error - usage is:", null,
optionSet);
}
}
var exitCode = 1;
try
{
switch (parseInput.LogFormat)
{
case LogFormat.VERBOSE:
((log4net.Repository.Hierarchy.Hierarchy) LogManager.GetRepository()).Root.Level =
Level.Debug;
((log4net.Repository.Hierarchy.Hierarchy) LogManager.GetRepository())
.RaiseConfigurationChanged(EventArgs.Empty);
break;
case LogFormat.SILENT:
((log4net.Repository.Hierarchy.Hierarchy) LogManager.GetRepository()).Root.Level =
Level.Off;
((log4net.Repository.Hierarchy.Hierarchy) LogManager.GetRepository())
.RaiseConfigurationChanged(EventArgs.Empty);
break;
case LogFormat.WARNING:
((log4net.Repository.Hierarchy.Hierarchy)LogManager.GetRepository()).Root.Level =
Level.Warn;
((log4net.Repository.Hierarchy.Hierarchy)LogManager.GetRepository())
.RaiseConfigurationChanged(EventArgs.Empty);
break;
case LogFormat.ERROR:
((log4net.Repository.Hierarchy.Hierarchy)LogManager.GetRepository()).Root.Level =
Level.Error;
((log4net.Repository.Hierarchy.Hierarchy)LogManager.GetRepository())
.RaiseConfigurationChanged(EventArgs.Empty);
break;
}
RawFileParser.Parse(parseInput);
Log.Info($"Processing completed {parseInput.Errors} errors, {parseInput.Warnings} warnings");
exitCode = parseInput.Vigilant ? parseInput.Errors + parseInput.Warnings: parseInput.Errors;
}
catch (UnauthorizedAccessException ex)
{
Log.Error(!ex.Message.IsNullOrEmpty()
? ex.Message
: "Attempting to write to an unauthorized location.");
}
catch (Amazon.S3.AmazonS3Exception ex)
{
Log.Error(!ex.Message.IsNullOrEmpty()
? "An Amazon S3 exception occured: " + ex.Message
: "An Amazon S3 exception occured: " + ex);
}
catch (Exception ex)
{
if (ex is RawFileParserException)
{
Log.Error(ex.Message);
}
else
{
Log.Error("An unexpected error occured:");
Log.Error(ex.ToString());
}
}
finally
{
Environment.Exit(exitCode);
}
}
/// <summary>
/// Show the help message
/// </summary>
/// <param name="message">the help message</param>
/// <param name="optionException">the option exception, can be null</param>
/// <param name="optionSet">the option set object</param>
private static void ShowHelp(string message, OptionException optionException, OptionSet optionSet)
{
if (optionException != null)
{
if (!optionException.OptionName.IsNullOrEmpty())
{
Console.Error.Write(optionException.OptionName + ": ");
}
Console.Error.WriteLine(optionException.Message);
}
Console.Error.WriteLine(message);
optionSet.WriteOptionDescriptions(Console.Error);
Environment.Exit(-1);
}
private static string GetValidEnumLevels(Type enumType)
{
List<string> output = new List<string>();
foreach (int v in Enum.GetValues(enumType))
{
output.Add(String.Format("{0} ({1})", Enum.GetName(enumType, v), v));
}
return String.Join("\n", output);
}
private static int ParseToEnum(Type enumType, string formatString, string keyName)
{
if (int.TryParse(formatString, out var formatInt)) //can be parsed as int
{
if (Enum.IsDefined(enumType, formatInt))
{
return formatInt;
}
else
{
throw new OptionException(
String.Format("unknown format value, the following values recognized (case insensitive)\n{0}", GetValidEnumLevels(enumType)),
keyName);
}
}
else //try parse as a string
{
try
{
return (int)Enum.Parse(enumType, formatString, true);
}
catch (Exception)
{
throw new OptionException(
String.Format("unknown format value, the following values recognized (case insensitive)\n{0}", GetValidEnumLevels(enumType)),
keyName);
}
}
}
private static HashSet<int> ParseMsLevel(string inputString)
{
HashSet<int> result = new HashSet<int>();
Regex valid = new Regex(@"^[\d,\-\s]+$");
Regex interval = new Regex(@"^\s*(\d+)?\s*(-)?\s*(\d+)?\s*$");
if (!valid.IsMatch(inputString))
throw new OptionException("Invalid characters in msLevel key", "msLevel");
foreach (var piece in inputString.Split(new char[] {','}))
{
try
{
int start;
int end;
var intervalMatch = interval.Match(piece);
if (!intervalMatch.Success)
throw new OptionException();
if (intervalMatch.Groups[2].Success) //it is interval
{
if (intervalMatch.Groups[1].Success)
start = Math.Max(1, int.Parse(intervalMatch.Groups[1].Value));
else
start = 1;
if (intervalMatch.Groups[3].Success)
end = Math.Min(10, int.Parse(intervalMatch.Groups[3].Value));
else
end = 10;
}
else
{
if (intervalMatch.Groups[1].Success)
end = start = int.Parse(intervalMatch.Groups[1].Value);
else
throw new OptionException();
if (intervalMatch.Groups[3].Success)
throw new OptionException();
}
for (int l = start; l <= end; l++)
{
result.Add(l);
}
}
catch (Exception ex)
{
throw new OptionException(String.Format("Cannot parse part of msLevel input: '{0}'", piece),
"msLevel", ex);
}
}
return result;
}
}
}