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caeteracaetera
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Merge branch 'keyword_cmd' into 1.4.0
2 parents 75876e2 + 4194520 commit 6cbb85a

36 files changed

+87560
-80
lines changed

‎MainClass.cs‎

Lines changed: 46 additions & 67 deletions
Original file line numberDiff line numberDiff line change
@@ -581,54 +581,12 @@ private static void RegularParametersParsing(string[] args)
581581

582582
if (outputFormatString != null)
583583
{
584-
int outPutFormatInt;
585-
try
586-
{
587-
outPutFormatInt = int.Parse(outputFormatString);
588-
}
589-
catch (FormatException)
590-
{
591-
throw new OptionException(
592-
"unknown output format value (0 for MGF, 1 for mzML, 2 for indexed mzML, 3 for Parquet)",
593-
"-f, --format");
594-
}
595-
596-
if (Enum.IsDefined(typeof(OutputFormat), outPutFormatInt) &&
597-
((OutputFormat) outPutFormatInt) != OutputFormat.NONE)
598-
{
599-
parseInput.OutputFormat = (OutputFormat) outPutFormatInt;
600-
}
601-
else
602-
{
603-
throw new OptionException(
604-
"unknown output format value (0 for MGF, 1 for mzML, 2 for indexed mzML, 3 for Parquet)",
605-
"-f, --format");
606-
}
584+
parseInput.OutputFormat = (OutputFormat)ParseToEnum(typeof(OutputFormat), outputFormatString, "-f, --format");
607585
}
608586

609587
if (metadataFormatString != null)
610588
{
611-
int metadataInt;
612-
try
613-
{
614-
metadataInt = int.Parse(metadataFormatString);
615-
}
616-
catch (FormatException)
617-
{
618-
throw new OptionException("unknown metadata format value (0 for JSON, 1 for TXT)",
619-
"-m, --metadata");
620-
}
621-
622-
if (Enum.IsDefined(typeof(MetadataFormat), metadataInt) &&
623-
((MetadataFormat) metadataInt) != MetadataFormat.NONE)
624-
{
625-
parseInput.MetadataFormat = (MetadataFormat) metadataInt;
626-
}
627-
else
628-
{
629-
throw new OptionException("unknown metadata format value (0 for JSON, 1 for TXT)",
630-
"-m, --metadata");
631-
}
589+
parseInput.MetadataFormat = (MetadataFormat)ParseToEnum(typeof(MetadataFormat), metadataFormatString, "-m, --metadata");
632590
}
633591

634592
if (parseInput.MetadataOutputFile != null && Directory.Exists(parseInput.MetadataOutputFile))
@@ -653,29 +611,7 @@ private static void RegularParametersParsing(string[] args)
653611

654612
if (logFormatString != null)
655613
{
656-
int logFormatInt;
657-
try
658-
{
659-
logFormatInt = int.Parse(logFormatString);
660-
}
661-
catch (FormatException)
662-
{
663-
throw new OptionException("unknown log format value (0 for silent, 1 for verbose)",
664-
"-l, --logging");
665-
}
666-
667-
if (Enum.IsDefined(typeof(LogFormat), logFormatInt))
668-
{
669-
if ((LogFormat) logFormatInt != LogFormat.NONE)
670-
{
671-
parseInput.LogFormat = (LogFormat) logFormatInt;
672-
}
673-
}
674-
else
675-
{
676-
throw new OptionException("unknown log format value (0 for silent, 1 for verbose)",
677-
"-l, --logging");
678-
}
614+
parseInput.LogFormat = (LogFormat)ParseToEnum(typeof(LogFormat), logFormatString, "-l, --logging");
679615
}
680616

681617
if (parseInput.StdOut)
@@ -789,6 +725,49 @@ private static void ShowHelp(string message, OptionException optionException, Op
789725
Environment.Exit(-1);
790726
}
791727

728+
private static string GetValidEnumLevels(Type enumType)
729+
{
730+
List<string> output = new List<string>();
731+
foreach (int v in Enum.GetValues(enumType))
732+
{
733+
output.Add(String.Format("{0} ({1})", Enum.GetName(enumType, v), v));
734+
}
735+
736+
return String.Join("\n", output);
737+
}
738+
739+
private static int ParseToEnum(Type enumType, string formatString, string keyName)
740+
{
741+
if (int.TryParse(formatString, out var formatInt)) //can be parsed as int
742+
{
743+
if (Enum.IsDefined(enumType, formatInt))
744+
{
745+
return formatInt;
746+
}
747+
else
748+
{
749+
throw new OptionException(
750+
String.Format("unknown format value, the following values recognized (case insensitive)\n{0}", GetValidEnumLevels(enumType)),
751+
keyName);
752+
}
753+
754+
}
755+
else //try parse as a string
756+
{
757+
try
758+
{
759+
return (int)Enum.Parse(enumType, formatString, true);
760+
}
761+
762+
catch (Exception)
763+
{
764+
throw new OptionException(
765+
String.Format("unknown format value, the following values recognized (case insensitive)\n{0}", GetValidEnumLevels(enumType)),
766+
keyName);
767+
}
768+
}
769+
}
770+
792771
private static HashSet<int> ParseMsLevel(string inputString)
793772
{
794773
HashSet<int> result = new HashSet<int>();

‎ThermoRawFileParser.csproj‎

Lines changed: 5 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,6 @@
11
<?xml version="1.0" encoding="utf-8"?>
22
<Project ToolsVersion="12.0" DefaultTargets="Build" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
3+
<Import Project="packages\NUnit3TestAdapter.4.1.0\build\net35\NUnit3TestAdapter.props" Condition="Exists('packages\NUnit3TestAdapter.4.1.0\build\net35\NUnit3TestAdapter.props')" />
34
<Import Project="packages\NUnit.3.13.1\build\NUnit.props" Condition="Exists('packages\NUnit.3.13.1\build\NUnit.props')" />
45
<Import Project="$(MSBuildExtensionsPath)\$(MSBuildToolsVersion)\Microsoft.Common.props" Condition="Exists('$(MSBuildExtensionsPath)\$(MSBuildToolsVersion)\Microsoft.Common.props')" />
56
<PropertyGroup>
@@ -14,6 +15,8 @@
1415
<TargetFrameworkVersion>v4.7.2</TargetFrameworkVersion>
1516
<FileAlignment>512</FileAlignment>
1617
<LangVersion>7.2</LangVersion>
18+
<NuGetPackageImportStamp>
19+
</NuGetPackageImportStamp>
1720
</PropertyGroup>
1821
<PropertyGroup Condition=" '$(Configuration)|$(Platform)' == 'Debug|AnyCPU' ">
1922
<PlatformTarget>x64</PlatformTarget>
@@ -242,6 +245,7 @@
242245
<ErrorText>This project references NuGet package(s) that are missing on this computer. Enable NuGet Package Restore to download them. For more information, see http://go.microsoft.com/fwlink/?LinkID=322105.The missing file is {0}.</ErrorText>
243246
</PropertyGroup>
244247
<Error Condition="!Exists('packages\NUnit.3.13.1\build\NUnit.props')" Text="$([System.String]::Format('$(ErrorText)', 'packages\NUnit.3.13.1\build\NUnit.props'))" />
248+
<Error Condition="!Exists('packages\NUnit3TestAdapter.4.1.0\build\net35\NUnit3TestAdapter.props')" Text="$([System.String]::Format('$(ErrorText)', 'packages\NUnit3TestAdapter.4.1.0\build\net35\NUnit3TestAdapter.props'))" />
245249
</Target>
246250
<!-- To modify your build process, add your task inside one of the targets below and uncomment it.
247251
Other similar extension points exist, see Microsoft.Common.targets.
@@ -250,4 +254,4 @@
250254
<Target Name="AfterBuild">
251255
</Target>
252256
-->
253-
</Project>
257+
</Project>

‎ThermoRawFileParserTest/ThermoRawFileParserTest.csproj‎

Lines changed: 9 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,7 @@
11
<?xml version="1.0" encoding="utf-8"?>
22
<Project ToolsVersion="12.0" DefaultTargets="Build" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
3-
<Import Project="..\packages\NUnit.3.13.1\build\NUnit.props" Condition="Exists('..\packages\NUnit.3.13.1\build\NUnit.props')" />
3+
<Import Project="..\packages\NUnit.3.13.2\build\NUnit.props" Condition="Exists('..\packages\NUnit.3.13.2\build\NUnit.props')" />
4+
<Import Project="..\packages\NUnit3TestAdapter.4.1.0\build\net35\NUnit3TestAdapter.props" Condition="Exists('..\packages\NUnit3TestAdapter.4.1.0\build\net35\NUnit3TestAdapter.props')" />
45
<Import Project="$(MSBuildExtensionsPath)\$(MSBuildToolsVersion)\Microsoft.Common.props" Condition="Exists('$(MSBuildExtensionsPath)\$(MSBuildToolsVersion)\Microsoft.Common.props')" />
56
<PropertyGroup>
67
<Configuration Condition=" '$(Configuration)' == '' ">Debug</Configuration>
@@ -14,9 +15,11 @@
1415
<TargetFrameworkVersion>v4.7.2</TargetFrameworkVersion>
1516
<FileAlignment>512</FileAlignment>
1617
<LangVersion>7.2</LangVersion>
18+
<NuGetPackageImportStamp>
19+
</NuGetPackageImportStamp>
1720
</PropertyGroup>
1821
<PropertyGroup Condition=" '$(Configuration)|$(Platform)' == 'Debug|AnyCPU' ">
19-
<PlatformTarget>AnyCPU</PlatformTarget>
22+
<PlatformTarget>x64</PlatformTarget>
2023
<DebugSymbols>true</DebugSymbols>
2124
<DebugType>full</DebugType>
2225
<Optimize>false</Optimize>
@@ -108,9 +111,8 @@
108111
<HintPath>..\packages\NJsonSchema.10.4.0\lib\net45\NJsonSchema.dll</HintPath>
109112
<Private>True</Private>
110113
</Reference>
111-
<Reference Include="nunit.framework, Version=3.13.1.0, Culture=neutral, PublicKeyToken=2638cd05610744eb">
112-
<HintPath>..\packages\NUnit.3.13.1\lib\net45\nunit.framework.dll</HintPath>
113-
<Private>True</Private>
114+
<Reference Include="nunit.framework, Version=3.13.2.0, Culture=neutral, PublicKeyToken=2638cd05610744eb, processorArchitecture=MSIL">
115+
<HintPath>..\packages\NUnit.3.13.2\lib\net45\nunit.framework.dll</HintPath>
114116
</Reference>
115117
<Reference Include="OpenMcdf, Version=2.2.1.9, Culture=neutral, PublicKeyToken=fdbb1629d7c00800, processorArchitecture=MSIL">
116118
<HintPath>..\packages\OpenMcdf.2.2.1.9\lib\net40\OpenMcdf.dll</HintPath>
@@ -229,8 +231,9 @@
229231
<PropertyGroup>
230232
<ErrorText>This project references NuGet package(s) that are missing on this computer. Enable NuGet Package Restore to download them. For more information, see http://go.microsoft.com/fwlink/?LinkID=322105.The missing file is {0}.</ErrorText>
231233
</PropertyGroup>
232-
<Error Condition="!Exists('..\packages\NUnit.3.13.1\build\NUnit.props')" Text="$([System.String]::Format('$(ErrorText)', '..\packages\NUnit.3.13.1\build\NUnit.props'))" />
233234
<Error Condition="!Exists('..\packages\mzLib.1.0.450\build\net471\mzLib.targets')" Text="$([System.String]::Format('$(ErrorText)', '..\packages\mzLib.1.0.450\build\net471\mzLib.targets'))" />
235+
<Error Condition="!Exists('..\packages\NUnit3TestAdapter.4.1.0\build\net35\NUnit3TestAdapter.props')" Text="$([System.String]::Format('$(ErrorText)', '..\packages\NUnit3TestAdapter.4.1.0\build\net35\NUnit3TestAdapter.props'))" />
236+
<Error Condition="!Exists('..\packages\NUnit.3.13.2\build\NUnit.props')" Text="$([System.String]::Format('$(ErrorText)', '..\packages\NUnit.3.13.2\build\NUnit.props'))" />
234237
</Target>
235238
<Import Project="..\packages\mzLib.1.0.450\build\net471\mzLib.targets" Condition="Exists('..\packages\mzLib.1.0.450\build\net471\mzLib.targets')" />
236239
<!-- To modify your build process, add your task inside one of the targets below and uncomment it.

‎ThermoRawFileParserTest/packages.config‎

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -11,7 +11,8 @@
1111
<package id="Namotion.Reflection" version="1.0.18" targetFramework="net472" />
1212
<package id="Newtonsoft.Json" version="13.0.1" targetFramework="net472" />
1313
<package id="NJsonSchema" version="10.4.0" targetFramework="net472" />
14-
<package id="NUnit" version="3.13.1" targetFramework="net472" />
14+
<package id="NUnit" version="3.13.2" targetFramework="net472" />
15+
<package id="NUnit3TestAdapter" version="4.1.0" targetFramework="net472" />
1516
<package id="OpenMcdf" version="2.2.1.9" targetFramework="net472" />
1617
<package id="OpenMcdf.Extensions" version="2.2.1.4" targetFramework="net472" />
1718
<package id="PSI_Interface" version="2.3.2" targetFramework="net472" />

‎packages.config‎

Lines changed: 6 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -4,22 +4,23 @@
44
<package id="AWSSDK.CloudWatchLogs" version="3.3.101.14" targetFramework="net472" />
55
<package id="AWSSDK.Core" version="3.3.103.30" targetFramework="net472" />
66
<package id="AWSSDK.S3" version="3.3.104.18" targetFramework="net472" />
7-
<package id="Parquet.Net" version="2.0.0" targetFramework="net472" />
87
<package id="IronSnappy" version="1.3.0" targetFramework="net472" />
9-
<package id="System.Buffers" version="4.5.1" targetFramework="net472" />
10-
<package id="System.Memory" version="4.5.4" targetFramework="net472" />
11-
<package id="System.Numerics.Vectors" version="4.5.0" targetFramework="net472" />
12-
<package id="System.Reflection.Emit.Lightweight" version="4.7.0" targetFramework="net472" />
138
<package id="log4net" version="2.0.12" targetFramework="net472" />
149
<package id="MathNet.Numerics" version="4.15.0" targetFramework="net472" />
1510
<package id="Mono.Options" version="6.6.0.161" targetFramework="net472" />
1611
<package id="Namotion.Reflection" version="1.0.18" targetFramework="net472" />
1712
<package id="Newtonsoft.Json" version="13.0.1" targetFramework="net472" />
1813
<package id="NJsonSchema" version="10.4.0" targetFramework="net472" />
1914
<package id="NUnit" version="3.13.1" targetFramework="net472" />
15+
<package id="NUnit3TestAdapter" version="4.1.0" targetFramework="net472" />
2016
<package id="OpenMcdf" version="2.2.1.9" targetFramework="net472" />
2117
<package id="OpenMcdf.Extensions" version="2.2.1.4" targetFramework="net472" />
18+
<package id="Parquet.Net" version="2.0.0" targetFramework="net472" />
19+
<package id="System.Buffers" version="4.5.1" targetFramework="net472" />
2220
<package id="System.IO.FileSystem.AccessControl" version="5.0.0" targetFramework="net472" />
21+
<package id="System.Memory" version="4.5.4" targetFramework="net472" />
22+
<package id="System.Numerics.Vectors" version="4.5.0" targetFramework="net472" />
23+
<package id="System.Reflection.Emit.Lightweight" version="4.7.0" targetFramework="net472" />
2324
<package id="System.Runtime.CompilerServices.Unsafe" version="5.0.0" targetFramework="net472" />
2425
<package id="System.Security.AccessControl" version="5.0.0" targetFramework="net472" />
2526
<package id="System.Security.Principal.Windows" version="5.0.0" targetFramework="net472" />

‎packages/NUnit.3.13.2/.signature.p7s‎

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