CompOmics · caetera · Oct 18, 2024 · Oct 22, 2024 · Oct 22, 2024 · Nov 15, 2024
diff --git a/.github/workflows/buildandtest.yml b/.github/workflows/buildandtest.yml
@@ -0,0 +1,46 @@
+name: buildtest
+
+on:
+  push:
+    paths:
+      - '**.cs'
+      - '.github/workflows/*.yml'
+  pull_request:
+    paths:
+      - '**.cs'
+      - '.github/workflows/*.yml'
+
+jobs:
+  buildandtest:
+
+    runs-on: 'ubuntu-latest'
+
+    steps:
+    - uses: actions/checkout@v4    
+      with:
+        path: 'main'
+
+    - name: Setup .NET
+      uses: actions/setup-dotnet@v4
+      with:
+        dotnet-version: 8.0.x
+
+    - name: Get Thermo packages
+      uses: actions/checkout@v4
+      with:
+        repository: 'thermofisherlsms/RawFileReader'
+        path: 'ThermoPKG'
+        token: ${{ secrets.GITHUB_TOKEN }}
+        sparse-checkout: 'Libs/NetCore/Net8/*.nupkg'
+        sparse-checkout-cone-mode: 'false'       
+
+    - name: Add Thermo packages as NuGet source
+      run: |
+        dotnet nuget add source -n ThermoPKG `pwd`/ThermoPKG/Libs/NetCore/Net8
+
+    - name: Build and test
+      run: |
+        cd main
+        dotnet build .
+        dotnet test .     
+
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -0,0 +1,93 @@
+name: publish
+
+on:
+  release:
+    types: 'published'
+
+jobs:
+  publish:
+
+    runs-on: 'ubuntu-latest'
+
+    steps:    
+    - uses: actions/checkout@v4
+      with:
+        path: 'main'
+
+    - name: Setup .NET
+      uses: actions/setup-dotnet@v4
+      with:
+        dotnet-version: 8.0.x
+
+    - name: Get Thermo packages
+      uses: actions/checkout@v4
+      with:
+        repository: 'thermofisherlsms/RawFileReader'
+        path: 'ThermoPKG'
+        token: ${{ secrets.GITHUB_TOKEN }}
+        sparse-checkout: 'Libs/NetCore/Net8/*.nupkg'
+        sparse-checkout-cone-mode: 'false'
+
+    - name: Add Thermo packages as NuGet source
+      run: |
+        dotnet nuget add source -n ThermoPKG `pwd`/ThermoPKG/Libs/NetCore/Net8
+
+    - name: Publish all
+      run: |
+        dotnet publish --configuration Release --runtime linux-x64 main/ThermoRawFileParser.csproj --sc -o publish/linux-x64
+        dotnet publish --configuration Release --runtime win-x64 main/ThermoRawFileParser.csproj --sc -o publish/win-x64
+        dotnet publish --configuration Release --runtime osx-x64 main/ThermoRawFileParser.csproj --sc -o publish/osx-x64
+        dotnet publish --configuration Release --framework net8.0 main/ThermoRawFileParser.csproj -o publish/net8
+
+    - name: Zipping Linux standalone
+      uses: vimtor/[email protected]
+      with:
+        files: publish/linux-x64
+        dest: ThermoRawFileParser-${{ github.ref_name }}-linux.zip
+
+    - name: Upload Linux to release
+      uses: svenstaro/upload-release-action@v2
+      with:
+        repo_token: ${{ secrets.GITHUB_TOKEN }}
+        file: ThermoRawFileParser-${{ github.ref_name }}-linux.zip
+        tag: ${{ github.ref }}
+
+    - name: Zipping OSX standalone
+      uses: vimtor/[email protected]
+      with:
+        files: publish/osx-x64
+        dest: ThermoRawFileParser-${{ github.ref_name }}-osx.zip
+
+    - name: Upload OSX to release
+      uses: svenstaro/upload-release-action@v2
+      with:
+        repo_token: ${{ secrets.GITHUB_TOKEN }}
+        file: ThermoRawFileParser-${{ github.ref_name }}-osx.zip
+        tag: ${{ github.ref }}
+
+    - name: Zipping Windows standalone
+      uses: vimtor/[email protected]
+      with:
+        files: publish/win-x64
+        dest: ThermoRawFileParser-${{ github.ref_name }}-win.zip
+
+    - name: Upload Windows to release
+      uses: svenstaro/upload-release-action@v2
+      with:
+        repo_token: ${{ secrets.GITHUB_TOKEN }}
+        file: ThermoRawFileParser-${{ github.ref_name }}-win.zip
+        tag: ${{ github.ref }}
+
+    - name: Zipping framework-based
+      uses: vimtor/[email protected]
+      with:
+        files: publish/net8
+        dest: ThermoRawFileParser-${{ github.ref_name }}-net8.zip
+
+    - name: Upload framework-based to release
+      uses: svenstaro/upload-release-action@v2
+      with:
+        repo_token: ${{ secrets.GITHUB_TOKEN }}
+        file: ThermoRawFileParser-${{ github.ref_name }}-net8.zip
+        tag: ${{ github.ref }}
+
diff --git a/.gitignore b/.gitignore
@@ -6,3 +6,4 @@ obj/
 .vs/
 *.csproj.user
 .vscode/
+Properties/
diff --git a/.travis.yml b/.travis.yml
diff --git a/.vs/ThermoRawFileParser/v15/.suo b/.vs/ThermoRawFileParser/v15/.suo
diff --git a/App.config b/App.config
@@ -1,44 +1,35 @@
 <?xml version="1.0" encoding="utf-8"?>
 <configuration>
+
+  <configSections>
+    <section name="log4net" type="System.Configuration.IgnoreSectionHandler" />
+  </configSections>
+
+  <log4net>
+    <root>
+      <level value="INFO" />
+      <appender-ref ref="console" />
+      <!-- <appender-ref ref="file" /> -->
+    </root>
+    <appender name="console" type="log4net.Appender.ConsoleAppender">
+      <layout type="log4net.Layout.PatternLayout">
+        <conversionPattern value="%date{yyyy-MM-dd HH:mm:ss} %level %message%newline" />
+      </layout>
+    </appender>
+    <!--<appender name="file" type="log4net.Appender.RollingFileAppender">        
+        <file value="ThermoRawFileParser.log" />
+        <appendToFile value="true" />
+        <rollingStyle value="Size" />
+        <maxSizeRollBackups value="5" />
+        <maximumFileSize value="10MB" />
+        <staticLogFileName value="true" />
+        <layout type="log4net.Layout.PatternLayout">
+            <conversionPattern value="%date{yyyy-MM-dd HH:mm:ss} [%thread] %message%newline" />
+        </layout>        
+    </appender>-->
+  </log4net>
+
   <runtime>
     <loadFromRemoteSources enabled="true" />
-    <assemblyBinding xmlns="urn:schemas-microsoft-com:asm.v1">
-      <dependentAssembly>
-        <assemblyIdentity name="System.Buffers" publicKeyToken="cc7b13ffcd2ddd51" culture="neutral" />
-        <bindingRedirect oldVersion="0.0.0.0-4.0.3.0" newVersion="4.0.3.0" />
-      </dependentAssembly>
-      <dependentAssembly>
-        <assemblyIdentity name="Newtonsoft.Json" publicKeyToken="30ad4fe6b2a6aeed" culture="neutral" />
-        <bindingRedirect oldVersion="0.0.0.0-13.0.0.0" newVersion="13.0.0.0" />
-      </dependentAssembly>
-      <dependentAssembly>
-        <assemblyIdentity name="OpenMcdf" publicKeyToken="fdbb1629d7c00800" culture="neutral" />
-        <bindingRedirect oldVersion="0.0.0.0-2.2.1.9" newVersion="2.2.1.9" />
-      </dependentAssembly>
-      <dependentAssembly>
-        <assemblyIdentity name="System.Runtime.CompilerServices.Unsafe" publicKeyToken="b03f5f7f11d50a3a" culture="neutral" />
-        <bindingRedirect oldVersion="0.0.0.0-5.0.0.0" newVersion="5.0.0.0" />
-      </dependentAssembly>
-      <dependentAssembly>
-        <assemblyIdentity name="ThermoFisher.CommonCore.Data" publicKeyToken="1aef06afb5abd953" culture="neutral" />
-        <bindingRedirect oldVersion="0.0.0.0-5.0.0.88" newVersion="5.0.0.88" />
-      </dependentAssembly>
-      <dependentAssembly>
-        <assemblyIdentity name="System.IO.FileSystem.AccessControl" publicKeyToken="b03f5f7f11d50a3a" culture="neutral" />
-        <bindingRedirect oldVersion="0.0.0.0-5.0.0.0" newVersion="5.0.0.0" />
-      </dependentAssembly>
-      <dependentAssembly>
-        <assemblyIdentity name="OpenMcdf.Extensions" publicKeyToken="fdbb1629d7c00800" culture="neutral" />
-        <bindingRedirect oldVersion="0.0.0.0-2.3.0.0" newVersion="2.3.0.0" />
-      </dependentAssembly>
-      <dependentAssembly>
-        <assemblyIdentity name="System.Security.Principal.Windows" publicKeyToken="b03f5f7f11d50a3a" culture="neutral" />
-        <bindingRedirect oldVersion="0.0.0.0-5.0.0.0" newVersion="5.0.0.0" />
-      </dependentAssembly>
-      <dependentAssembly>
-        <assemblyIdentity name="System.Security.AccessControl" publicKeyToken="b03f5f7f11d50a3a" culture="neutral" />
-        <bindingRedirect oldVersion="0.0.0.0-5.0.0.0" newVersion="5.0.0.0" />
-      </dependentAssembly>
-    </assemblyBinding>
   </runtime>
 </configuration>
diff --git a/MainClass.cs b/MainClass.cs
@@ -13,14 +13,16 @@
 using System.Text.RegularExpressions;
 using System.Data;
 
+[assembly: log4net.Config.XmlConfigurator()]
+
 namespace ThermoRawFileParser
 {
     public static class MainClass
     {
         private static readonly ILog Log =
-            LogManager.GetLogger(System.Reflection.MethodBase.GetCurrentMethod().DeclaringType);
+            LogManager.GetLogger(MethodBase.GetCurrentMethod().DeclaringType);
 
-        public const string Version = "1.4.5";
+        public static string Version = Assembly.GetExecutingAssembly().GetName().Version.ToString();
         public static void Main(string[] args)
         {
             // Set Invariant culture as default for all further processing
@@ -125,7 +127,7 @@ private static void XicParametersParsing(string[] args)
 
                 if (parameters.help)
                 {
-                    ShowHelp("usage is:", null,
+                    ShowHelp("usage is:", new OptionException(),
                         optionSet);
                     return;
                 }
@@ -253,12 +255,12 @@ private static void XicParametersParsing(string[] args)
             {
                 if (parameters.help)
                 {
-                    ShowHelp("usage is:", null,
+                    ShowHelp("usage is:", new OptionException(),
                         optionSet);
                 }
                 else
                 {
-                    ShowHelp("Error - usage is:", null,
+                    ShowHelp("Error - usage is:", new OptionException(),
                         optionSet);
                 }
             }
@@ -374,7 +376,7 @@ private static void SpectrumQueryParametersParsing(string[] args)
 
                 if (parameters.help)
                 {
-                    ShowHelp("usage is:", null,
+                    ShowHelp("usage is:", new OptionException(),
                         optionSet);
                     return;
                 }
@@ -416,12 +418,12 @@ private static void SpectrumQueryParametersParsing(string[] args)
             {
                 if (parameters.help)
                 {
-                    ShowHelp("usage is:", null,
+                    ShowHelp("usage is:", new OptionException(),
                         optionSet);
                 }
                 else
                 {
-                    ShowHelp("Error - usage is:", null,
+                    ShowHelp("Error - usage is:", new OptionException(),
                         optionSet);
                 }
             }
@@ -497,7 +499,7 @@ private static void RegularParametersParsing(string[] args)
                     h => help = h != null
                 },
                 {
-                    "version", "Prints out the version of the executable.",
+                    "v|version", "Prints out the version of the executable.",
                     v => version = v != null
                 },
                 {
@@ -583,6 +585,10 @@ private static void RegularParametersParsing(string[] args)
                     "N|noiseData", "Include noise data in mzML output",
                     v => parseInput.NoiseData = v != null
                 },
+                {
+                    "C|chargeData", "Include instrument detected charge states in mzML output (only for high resolution centroided data)",
+                    v => parseInput.ChargeData = v != null
+                },
                 {
                   "w|warningsAreErrors", "Return non-zero exit code for warnings; default only for errors",
                     v => parseInput.Vigilant = v != null 
@@ -623,7 +629,7 @@ private static void RegularParametersParsing(string[] args)
                 {
                     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);
+                    ShowHelp(helpMessage, new OptionException(), optionSet);
                     return;
                 }
 
@@ -766,6 +772,9 @@ private static void RegularParametersParsing(string[] args)
                     if (parseInput.OutputFormat == OutputFormat.IndexMzML) parseInput.OutputFormat = OutputFormat.MzML;
                 }
 
+                // Switch off gzip compression for Parquet
+                if (parseInput.OutputFormat == OutputFormat.Parquet) parseInput.Gzip = false;
+
                 parseInput.MaxLevel = parseInput.MsLevel.Max();
 
                 if (parseInput.S3Url != null && parseInput.S3AccessKeyId != null &&
@@ -788,12 +797,12 @@ private static void RegularParametersParsing(string[] args)
             {
                 if (help)
                 {
-                    ShowHelp("usage is:", null,
+                    ShowHelp("usage is:", new OptionException(),
                         optionSet);
                 }
                 else
                 {
-                    ShowHelp("Error - usage is:", null,
+                    ShowHelp("Error - usage is:", new OptionException(),
                         optionSet);
                 }
             }

diff --git a/ParseInput.cs b/ParseInput.cs
@@ -102,6 +102,8 @@ public int Warnings
 
         public bool NoiseData { get; set; }
 
+        public bool ChargeData { get; set; }
+
         public bool StdOut { get; set; }
 
         public bool Vigilant { get; set; }
@@ -135,6 +137,7 @@ public ParseInput()
             MgfPrecursor = false;
             StdOut = false;
             NoiseData = false;
+            ChargeData = false;
             Vigilant = false;
             _errors = 0;
             _warnings = 0;