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Merge branch 'master' into Issue98
2 parents 51bcb87 + f51d523 commit 53a8e7e

692 files changed

Lines changed: 528249 additions & 420099 deletions

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‎MainClass.cs‎

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -19,7 +19,7 @@ public static class MainClass
1919
private static readonly ILog Log =
2020
LogManager.GetLogger(System.Reflection.MethodBase.GetCurrentMethod().DeclaringType);
2121

22-
public const string Version = "1.3.2";
22+
public const string Version = "1.3.3";
2323

2424
public static void Main(string[] args)
2525
{
@@ -385,7 +385,7 @@ private static void RegularParametersParsing(string[] args)
385385
},
386386
{
387387
"f=|format=",
388-
"The spectra output format: 0 for MGF, 1 for mzML, 2 for indexed mzML, 3 for Parquet. Defaults to mzML if no format is specified.",
388+
"The spectra output format: 0 for MGF, 1 for mzML, 2 for indexed mzML, 3 for Parquet. Defaults to indexed mzML if no format is specified.",
389389
v => outputFormatString = v
390390
},
391391
{
@@ -430,13 +430,13 @@ private static void RegularParametersParsing(string[] args)
430430
},
431431
{
432432
"L=|msLevel=",
433-
"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",
433+
"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",
434434
v => parseInput.MsLevel = ParseMsLevel(v)
435435
},
436436
{
437437
"P|mgfPrecursor",
438438
"Include precursor scan number in MGF file TITLE",
439-
v => parseInput.MGFPrecursor = v != null
439+
v => parseInput.MgfPrecursor = v != null
440440
},
441441
{
442442
"u:|s3_url:",
@@ -565,7 +565,7 @@ private static void RegularParametersParsing(string[] args)
565565

566566
if (metadataFormatString == null && outputFormatString == null)
567567
{
568-
parseInput.OutputFormat = OutputFormat.MzML;
568+
parseInput.OutputFormat = OutputFormat.IndexMzML;
569569
}
570570

571571
if (outputFormatString != null)

‎OutputFormat.cs‎

Lines changed: 0 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -13,7 +13,6 @@ public enum MetadataFormat
1313
{
1414
JSON,
1515
TXT,
16-
PARQUET,
1716
NONE
1817
}
1918
}

‎ParseInput.cs‎

Lines changed: 11 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -7,13 +7,13 @@ namespace ThermoRawFileParser
77
{
88
public class ParseInput
99
{
10-
//all ms levels
11-
private readonly HashSet<int> allLevels = new HashSet<int>(new int[] { 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 });
10+
// All MS levels
11+
private readonly HashSet<int> _allLevels = new HashSet<int>(new int[] {1, 2, 3, 4, 5, 6, 7, 8, 9, 10});
1212

1313
/// <summary>
1414
/// The RAW file path.
1515
/// </summary>
16-
private string rawFilePath;
16+
private string _rawFilePath;
1717

1818
/// <summary>
1919
/// The RAW folder path.
@@ -22,15 +22,15 @@ public class ParseInput
2222

2323
public string RawFilePath
2424
{
25-
get => rawFilePath;
25+
get => _rawFilePath;
2626
set
2727
{
28-
rawFilePath = value;
28+
_rawFilePath = value;
2929
if (value != null)
3030
{
3131
RawFileNameWithoutExtension = Path.GetFileNameWithoutExtension(value);
3232
var splittedPath = value.Split('/');
33-
rawFileName = splittedPath[splittedPath.Length - 1];
33+
_rawFileName = splittedPath[splittedPath.Length - 1];
3434
}
3535
}
3636
}
@@ -79,7 +79,7 @@ public string RawFilePath
7979

8080
public HashSet<int> MsLevel { get; set; }
8181

82-
public bool MGFPrecursor { get; set; }
82+
public bool MgfPrecursor { get; set; }
8383

8484
private S3Loader S3Loader { get; set; }
8585

@@ -94,7 +94,7 @@ public string RawFilePath
9494
/// <summary>
9595
/// The raw file name.
9696
/// </summary>
97-
private string rawFileName;
97+
private string _rawFileName;
9898

9999
/// <summary>
100100
/// The RAW file name without extension.
@@ -111,7 +111,8 @@ public ParseInput()
111111
LogFormat = LogFormat.DEFAULT;
112112
IgnoreInstrumentErrors = false;
113113
AllDetectors = false;
114-
MsLevel = allLevels;
114+
MsLevel = _allLevels;
115+
MgfPrecursor = false;
115116
}
116117

117118
public ParseInput(string rawFilePath, string rawDirectoryPath, string outputDirectory, OutputFormat outputFormat
@@ -121,6 +122,7 @@ public ParseInput(string rawFilePath, string rawDirectoryPath, string outputDire
121122
RawDirectoryPath = rawDirectoryPath;
122123
OutputDirectory = outputDirectory;
123124
OutputFormat = outputFormat;
125+
MgfPrecursor = true;
124126
}
125127

126128
public void InitializeS3Bucket()

‎Properties/AssemblyInfo.cs‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -31,7 +31,7 @@
3131
// You can specify all the values or you can default the Build and Revision Numbers
3232
// by using the '*' as shown below:
3333
// [assembly: AssemblyVersion("1.0.*")]
34-
[assembly: AssemblyVersion("1.3.2.0")]
35-
[assembly: AssemblyFileVersion("1.3.2.0")]
34+
[assembly: AssemblyVersion("1.3.3.0")]
35+
[assembly: AssemblyFileVersion("1.3.3.0")]
3636

3737
[assembly: log4net.Config.XmlConfigurator(ConfigFile = "log4net.config")]

‎README.md‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -121,7 +121,7 @@ Return one or more chromatograms based on query JSON input.
121121
mono ThermoRawFileParser.exe xic -i=/home/user/data_input/raw_file.raw -j=/home/user/xic_input.json
122122
```
123123
```
124-
ThermoRawFileParser.exe query --help
124+
ThermoRawFileParser.exe xic --help
125125
usage is:
126126
-h, --help Prints out the options.
127127
-i, --input=VALUE The raw file input (Required). Specify this or an

‎ThermoRawFileParser.csproj‎

Lines changed: 73 additions & 33 deletions
Original file line numberDiff line numberDiff line change
@@ -1,6 +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\NUnit.3.12.0\build\NUnit.props" Condition="Exists('packages\NUnit.3.12.0\build\NUnit.props')" />
3+
<Import Project="packages\NUnit.3.13.1\build\NUnit.props" Condition="Exists('packages\NUnit.3.13.1\build\NUnit.props')" />
44
<Import Project="$(MSBuildExtensionsPath)\$(MSBuildToolsVersion)\Microsoft.Common.props" Condition="Exists('$(MSBuildExtensionsPath)\$(MSBuildToolsVersion)\Microsoft.Common.props')" />
55
<PropertyGroup>
66
<Configuration Condition=" '$(Configuration)' == '' ">Debug</Configuration>
@@ -60,81 +60,121 @@
6060
<StartupObject>ThermoRawFileParser.MainClass</StartupObject>
6161
</PropertyGroup>
6262
<ItemGroup>
63-
<Reference Include="AWS.Logger.Core, Version=1.4.0.0, Culture=neutral, PublicKeyToken=885c28607f98e604">
64-
<HintPath>packages\AWS.Logger.Core.1.4.0\lib\net45\AWS.Logger.Core.dll</HintPath>
63+
<Reference Include="AWS.Logger.Core, Version=2.0.1.0, Culture=neutral, PublicKeyToken=885c28607f98e604">
64+
<HintPath>packages\AWS.Logger.Core.2.0.1\lib\net45\AWS.Logger.Core.dll</HintPath>
6565
<Private>True</Private>
6666
</Reference>
6767
<Reference Include="AWSSDK.CloudWatchLogs, Version=3.3.0.0, Culture=neutral, PublicKeyToken=885c28607f98e604">
68-
<HintPath>packages\AWSSDK.CloudWatchLogs.3.3.101.14\lib\net45\AWSSDK.CloudWatchLogs.dll</HintPath>
68+
<HintPath>packages\AWSSDK.CloudWatchLogs.3.5.0.24\lib\net45\AWSSDK.CloudWatchLogs.dll</HintPath>
6969
<Private>True</Private>
7070
</Reference>
7171
<Reference Include="AWSSDK.Core, Version=3.3.0.0, Culture=neutral, PublicKeyToken=885c28607f98e604">
72-
<HintPath>packages\AWSSDK.Core.3.3.103.30\lib\net45\AWSSDK.Core.dll</HintPath>
72+
<HintPath>packages\AWSSDK.Core.3.5.3.2\lib\net45\AWSSDK.Core.dll</HintPath>
7373
<Private>True</Private>
7474
</Reference>
7575
<Reference Include="AWSSDK.S3, Version=3.3.0.0, Culture=neutral, PublicKeyToken=885c28607f98e604">
76-
<HintPath>packages\AWSSDK.S3.3.3.104.18\lib\net45\AWSSDK.S3.dll</HintPath>
76+
<HintPath>packages\AWSSDK.S3.3.5.8.8\lib\net45\AWSSDK.S3.dll</HintPath>
7777
<Private>True</Private>
7878
</Reference>
79-
<Reference Include="log4net, Version=2.0.8.0, Culture=neutral, PublicKeyToken=669e0ddf0bb1aa2a">
80-
<HintPath>packages\log4net.2.0.8\lib\net45-full\log4net.dll</HintPath>
79+
<Reference Include="IronSnappy, Version=1.3.0.0, Culture=neutral, PublicKeyToken=b1d4b1dc83bdcf31">
80+
<HintPath>packages\IronSnappy.1.3.0\lib\netstandard2.0\IronSnappy.dll</HintPath>
81+
<Private>True</Private>
82+
</Reference>
83+
<Reference Include="log4net, Version=2.0.12.0, Culture=neutral, PublicKeyToken=669e0ddf0bb1aa2a">
84+
<HintPath>packages\log4net.2.0.12\lib\net45\log4net.dll</HintPath>
85+
<Private>True</Private>
8186
</Reference>
82-
<Reference Include="MathNet.Numerics, Version=4.8.1.0, Culture=neutral, PublicKeyToken=null">
83-
<HintPath>packages\MathNet.Numerics.4.8.1\lib\net461\MathNet.Numerics.dll</HintPath>
87+
<Reference Include="MathNet.Numerics, Version=4.15.0.0, Culture=neutral, PublicKeyToken=null">
88+
<HintPath>packages\MathNet.Numerics.4.15.0\lib\net461\MathNet.Numerics.dll</HintPath>
8489
<Private>True</Private>
8590
</Reference>
8691
<Reference Include="Microsoft.CSharp" />
87-
<Reference Include="Mono.Options, Version=5.0.0.0, Culture=neutral, PublicKeyToken=null">
88-
<HintPath>packages\Mono.Options.5.3.0.1\lib\net4-client\Mono.Options.dll</HintPath>
92+
<Reference Include="Mono.Options, Version=6.0.0.0, Culture=neutral, PublicKeyToken=null">
93+
<HintPath>packages\Mono.Options.6.6.0.161\lib\net40\Mono.Options.dll</HintPath>
94+
<Private>True</Private>
8995
</Reference>
9096
<Reference Include="mscorlib" />
91-
<Reference Include="Namotion.Reflection, Version=1.0.8.0, Culture=neutral, PublicKeyToken=c2f9c3bdfae56102">
92-
<HintPath>packages\Namotion.Reflection.1.0.8\lib\net45\Namotion.Reflection.dll</HintPath>
97+
<Reference Include="Namotion.Reflection, Version=1.0.18.0, Culture=neutral, PublicKeyToken=c2f9c3bdfae56102">
98+
<HintPath>packages\Namotion.Reflection.1.0.18\lib\net45\Namotion.Reflection.dll</HintPath>
9399
<Private>True</Private>
94100
</Reference>
95101
<Reference Include="Newtonsoft.Json, Version=12.0.0.0, Culture=neutral, PublicKeyToken=30ad4fe6b2a6aeed">
96-
<HintPath>packages\Newtonsoft.Json.12.0.2\lib\net45\Newtonsoft.Json.dll</HintPath>
102+
<HintPath>packages\Newtonsoft.Json.12.0.3\lib\net45\Newtonsoft.Json.dll</HintPath>
103+
<Private>True</Private>
104+
</Reference>
105+
<Reference Include="NJsonSchema, Version=10.3.8.0, Culture=neutral, PublicKeyToken=c2f9c3bdfae56102">
106+
<HintPath>packages\NJsonSchema.10.3.8\lib\net45\NJsonSchema.dll</HintPath>
97107
<Private>True</Private>
98108
</Reference>
99-
<Reference Include="NJsonSchema, Version=10.1.5.0, Culture=neutral, PublicKeyToken=c2f9c3bdfae56102">
100-
<HintPath>packages\NJsonSchema.10.1.5\lib\net45\NJsonSchema.dll</HintPath>
109+
<Reference Include="nunit.framework, Version=3.13.1.0, Culture=neutral, PublicKeyToken=2638cd05610744eb">
110+
<HintPath>packages\NUnit.3.13.1\lib\net45\nunit.framework.dll</HintPath>
101111
<Private>True</Private>
102112
</Reference>
103-
<Reference Include="nunit.framework, Version=3.12.0.0, Culture=neutral, PublicKeyToken=2638cd05610744eb">
104-
<HintPath>packages\NUnit.3.12.0\lib\net45\nunit.framework.dll</HintPath>
113+
<Reference Include="OpenMcdf, Version=2.2.1.9, Culture=neutral, PublicKeyToken=fdbb1629d7c00800">
114+
<HintPath>packages\OpenMcdf.2.2.1.9\lib\net40\OpenMcdf.dll</HintPath>
105115
<Private>True</Private>
106116
</Reference>
107-
<Reference Include="Parquet, Version=2.0.0.0, Culture=neutral, PublicKeyToken=de28deb604dd91c9, processorArchitecture=MSIL">
117+
<Reference Include="OpenMcdf.Extensions, Version=2.3.0.0, Culture=neutral, PublicKeyToken=fdbb1629d7c00800">
118+
<HintPath>packages\OpenMcdf.Extensions.2.2.1.4\lib\net40\OpenMcdf.Extensions.dll</HintPath>
119+
<Private>True</Private>
120+
</Reference>
121+
<Reference Include="Parquet, Version=2.0.0.0, Culture=neutral, PublicKeyToken=de28deb604dd91c9">
108122
<HintPath>packages\Parquet.Net.2.0.0\lib\net451\Parquet.dll</HintPath>
123+
<Private>True</Private>
109124
</Reference>
110125
<Reference Include="System" />
126+
<Reference Include="System.Buffers, Version=4.0.3.0, Culture=neutral, PublicKeyToken=cc7b13ffcd2ddd51">
127+
<HintPath>packages\System.Buffers.4.5.1\lib\net461\System.Buffers.dll</HintPath>
128+
<Private>True</Private>
129+
</Reference>
111130
<Reference Include="System.ComponentModel.DataAnnotations" />
131+
<Reference Include="System.Configuration" />
112132
<Reference Include="System.Core" />
133+
<Reference Include="System.IO.FileSystem.AccessControl, Version=5.0.0.0, Culture=neutral, PublicKeyToken=b03f5f7f11d50a3a">
134+
<HintPath>packages\System.IO.FileSystem.AccessControl.5.0.0\lib\net461\System.IO.FileSystem.AccessControl.dll</HintPath>
135+
<Private>True</Private>
136+
</Reference>
137+
<Reference Include="System.Memory, Version=4.0.1.1, Culture=neutral, PublicKeyToken=cc7b13ffcd2ddd51">
138+
<HintPath>packages\System.Memory.4.5.4\lib\net461\System.Memory.dll</HintPath>
139+
<Private>True</Private>
140+
</Reference>
113141
<Reference Include="System.Net" />
114142
<Reference Include="System.Numerics" />
115-
<Reference Include="System.Runtime.CompilerServices.Unsafe, Version=4.0.4.1, Culture=neutral, PublicKeyToken=b03f5f7f11d50a3a">
116-
<HintPath>packages\System.Runtime.CompilerServices.Unsafe.4.5.2\lib\netstandard2.0\System.Runtime.CompilerServices.Unsafe.dll</HintPath>
143+
<Reference Include="System.Numerics.Vectors, Version=4.1.4.0, Culture=neutral, PublicKeyToken=b03f5f7f11d50a3a">
144+
<HintPath>packages\System.Numerics.Vectors.4.5.0\lib\net46\System.Numerics.Vectors.dll</HintPath>
145+
<Private>True</Private>
146+
</Reference>
147+
<Reference Include="System.Runtime.CompilerServices.Unsafe, Version=5.0.0.0, Culture=neutral, PublicKeyToken=b03f5f7f11d50a3a">
148+
<HintPath>packages\System.Runtime.CompilerServices.Unsafe.5.0.0\lib\net45\System.Runtime.CompilerServices.Unsafe.dll</HintPath>
117149
<Private>True</Private>
118150
</Reference>
119151
<Reference Include="System.Runtime.Serialization" />
120-
<Reference Include="System.Text.Encoding.CodePages, Version=4.1.1.0, Culture=neutral, PublicKeyToken=b03f5f7f11d50a3a">
121-
<HintPath>packages\System.Text.Encoding.CodePages.4.5.1\lib\net461\System.Text.Encoding.CodePages.dll</HintPath>
152+
<Reference Include="System.Security.AccessControl, Version=5.0.0.0, Culture=neutral, PublicKeyToken=b03f5f7f11d50a3a">
153+
<HintPath>packages\System.Security.AccessControl.5.0.0\lib\net461\System.Security.AccessControl.dll</HintPath>
154+
<Private>True</Private>
155+
</Reference>
156+
<Reference Include="System.Security.Principal.Windows, Version=5.0.0.0, Culture=neutral, PublicKeyToken=b03f5f7f11d50a3a">
157+
<HintPath>packages\System.Security.Principal.Windows.5.0.0\lib\net461\System.Security.Principal.Windows.dll</HintPath>
158+
<Private>True</Private>
159+
</Reference>
160+
<Reference Include="System.Text.Encoding.CodePages, Version=5.0.0.0, Culture=neutral, PublicKeyToken=b03f5f7f11d50a3a">
161+
<HintPath>packages\System.Text.Encoding.CodePages.5.0.0\lib\net461\System.Text.Encoding.CodePages.dll</HintPath>
122162
<Private>True</Private>
123163
</Reference>
124164
<Reference Include="System.ValueTuple, Version=4.0.3.0, Culture=neutral, PublicKeyToken=cc7b13ffcd2ddd51">
125165
<HintPath>packages\System.ValueTuple.4.5.0\lib\net47\System.ValueTuple.dll</HintPath>
126166
<Private>True</Private>
127167
</Reference>
168+
<Reference Include="System.Web" />
128169
<Reference Include="System.Xml.Linq" />
129170
<Reference Include="System.Data.DataSetExtensions" />
130171
<Reference Include="System.Data" />
131172
<Reference Include="System.Xml" />
132-
<Reference Include="ThermoFisher.CommonCore.Data, Version=5.0.0.38, Culture=neutral, PublicKeyToken=1aef06afb5abd953">
133-
<HintPath>packages\ThermoFisher.CommonCore.Data.5.0.0.38\lib\net471\ThermoFisher.CommonCore.Data.dll</HintPath>
173+
<Reference Include="ThermoFisher.CommonCore.Data, Version=5.0.0.71, Culture=neutral, PublicKeyToken=1aef06afb5abd953, processorArchitecture=MSIL">
174+
<HintPath>packages\ThermoFisher.CommonCore.Data.5.0.0.71\lib\netstandard2.0\ThermoFisher.CommonCore.Data.dll</HintPath>
134175
</Reference>
135-
<Reference Include="ThermoFisher.CommonCore.RawFileReader, Version=5.0.0.38, Culture=neutral, PublicKeyToken=1aef06afb5abd953">
136-
<HintPath>packages\ThermoFisher.CommonCore.RawFileReader.5.0.0.38\lib\net471\ThermoFisher.CommonCore.RawFileReader.dll</HintPath>
137-
<Private>True</Private>
176+
<Reference Include="ThermoFisher.CommonCore.RawFileReader, Version=5.0.0.71, Culture=neutral, PublicKeyToken=1aef06afb5abd953, processorArchitecture=MSIL">
177+
<HintPath>packages\ThermoFisher.CommonCore.RawFileReader.5.0.0.71\lib\netstandard2.0\ThermoFisher.CommonCore.RawFileReader.dll</HintPath>
138178
</Reference>
139179
<Reference Include="zlib.net, Version=1.0.3.0, Culture=neutral, PublicKeyToken=47d7877cb3620160">
140180
<HintPath>packages\zlib.net.1.0.4.0\lib\zlib.net.dll</HintPath>
@@ -186,15 +226,15 @@
186226
<Content Include="Writer\MzML\mzML1.1.1_idx.xsd" />
187227
</ItemGroup>
188228
<ItemGroup>
189-
<Analyzer Include="packages\AWSSDK.CloudWatchLogs.3.3.101.14\analyzers\dotnet\cs\AWSSDK.CloudWatchLogs.CodeAnalysis.dll" />
190-
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229+
<Analyzer Include="packages\AWSSDK.CloudWatchLogs.3.5.0.24\analyzers\dotnet\cs\AWSSDK.CloudWatchLogs.CodeAnalysis.dll" />
230+
<Analyzer Include="packages\AWSSDK.S3.3.5.8.8\analyzers\dotnet\cs\AWSSDK.S3.CodeAnalysis.dll" />
191231
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192232
<Import Project="$(MSBuildToolsPath)\Microsoft.CSharp.targets" />
193233
<Target Name="EnsureNuGetPackageBuildImports" BeforeTargets="PrepareForBuild">
194234
<PropertyGroup>
195235
<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>
196236
</PropertyGroup>
197-
<Error Condition="!Exists('packages\NUnit.3.12.0\build\NUnit.props')" Text="$([System.String]::Format('$(ErrorText)', 'packages\NUnit.3.12.0\build\NUnit.props'))" />
237+
<Error Condition="!Exists('packages\NUnit.3.13.1\build\NUnit.props')" Text="$([System.String]::Format('$(ErrorText)', 'packages\NUnit.3.13.1\build\NUnit.props'))" />
198238
</Target>
199239
<!-- To modify your build process, add your task inside one of the targets below and uncomment it.
200240
Other similar extension points exist, see Microsoft.Common.targets.
@@ -203,4 +243,4 @@
203243
<Target Name="AfterBuild">
204244
</Target>
205245
-->
206-
</Project>
246+
</Project>

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