mzlib update to fix filename mismatch and failure to load ids (#118)

* mzlib update and shift to x64 * mzlib 535 * periodTolerantFilename * variable rename * vxc * name simplified * style * configuration manager changes * netserializer 4.1.2 Co-authored-by: MICHAEL SHORTREED <mrshortreed@wisc.edu>
smith-chem-wisc · Sep 16, 2022 · eba779a · eba779a
1 parent b6b5496
commit eba779a
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Showing 10 changed files with 39 additions and 35 deletions.
diff --git a/CMD/CMD.csproj b/CMD/CMD.csproj
@@ -11,13 +11,14 @@
     <GenerateAssemblyVersionAttribute>false</GenerateAssemblyVersionAttribute>
     <GenerateAssemblyFileVersionAttribute>false</GenerateAssemblyFileVersionAttribute>
     <ApplicationIcon>FlashLFQ_Icon.ico</ApplicationIcon>
+    <Platforms>AnyCPU</Platforms>
   </PropertyGroup>
 
   <ItemGroup>
     <PackageReference Include="CommandLineParser" Version="2.7.82" />
-    <PackageReference Include="MathNet.Numerics" Version="4.9.0" />
-    <PackageReference Include="mzLib" Version="1.0.529" />
-    <PackageReference Include="NetSerializer" Version="4.1.1" />
+    <PackageReference Include="MathNet.Numerics" Version="5.0.0" />
+    <PackageReference Include="mzLib" Version="1.0.535" />
+    <PackageReference Include="NetSerializer" Version="4.1.2" />
     <PackageReference Include="Nett" Version="0.15.0" />
     <PackageReference Include="SharpLearning.Common.Interfaces" Version="0.28.0" />
     <PackageReference Include="SharpLearning.Containers" Version="0.28.0" />

diff --git a/CMD/FlashLFQExecutable.cs b/CMD/FlashLFQExecutable.cs
@@ -2,9 +2,9 @@
 using CommandLine.Text;
 using FlashLFQ;
 using IO.ThermoRawFileReader;
+using MzLibUtil;
 using System;
 using System.Collections.Generic;
-using System.Diagnostics;
 using System.IO;
 using System.Linq;
 using Util;
@@ -69,11 +69,11 @@ private static void Run(FlashLfqSettings settings)
                 .Where(f => acceptedSpectrumFileFormats.Contains(Path.GetExtension(f).ToLowerInvariant())).ToList();
 
             // check for duplicate file names (agnostic of file extension)
-            foreach (var fileNameWithoutExtension in filePaths.GroupBy(p => Path.GetFileNameWithoutExtension(p)))
+            foreach (var fileNameWithoutExtension in filePaths.GroupBy(p => PeriodTolerantFilenameWithoutExtension.GetPeriodTolerantFilenameWithoutExtension(p)))
             {
                 if (fileNameWithoutExtension.Count() > 1)
                 {
-                    var types = fileNameWithoutExtension.Select(p => Path.GetFileNameWithoutExtension(p)).Distinct();
+                    var types = fileNameWithoutExtension.Select(p => PeriodTolerantFilenameWithoutExtension.GetPeriodTolerantFilenameWithoutExtension(p)).Distinct();
 
                     if (!settings.Silent)
                     {
@@ -140,9 +140,9 @@ private static void Run(FlashLfqSettings settings)
                 var experimentalDesign = File.ReadAllLines(assumedPathToExpDesign)
                     .ToDictionary(v => v.Split('\t')[0], v => v);
 
-                foreach (var file in filePaths)
+                foreach (var filePath in filePaths)
                 {
-                    string fileNameWithoutExtension = Path.GetFileNameWithoutExtension(file);
+                    string fileNameWithoutExtension = PeriodTolerantFilenameWithoutExtension.GetPeriodTolerantFilenameWithoutExtension(filePath);
 
                     var expDesignForThisFile = experimentalDesign[fileNameWithoutExtension];
                     var split = expDesignForThisFile.Split('\t');
@@ -153,7 +153,7 @@ private static void Run(FlashLfqSettings settings)
                     int techrep = int.Parse(split[4]);
 
                     // experimental design info passed in here for each spectra file
-                    spectraFileInfos.Add(new SpectraFileInfo(fullFilePathWithExtension: file,
+                    spectraFileInfos.Add(new SpectraFileInfo(fullFilePathWithExtension: filePath,
                         condition: condition,
                         biorep: biorep - 1,
                         fraction: fraction - 1,

diff --git a/FlashLFQ.sln b/FlashLFQ.sln
@@ -1,15 +1,15 @@
 
 Microsoft Visual Studio Solution File, Format Version 12.00
-# Visual Studio Version 16
-VisualStudioVersion = 16.0.29418.71
+# Visual Studio Version 17
+VisualStudioVersion = 17.3.32825.248
 MinimumVisualStudioVersion = 10.0.40219.1
-Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "GUI", "GUI\GUI.csproj", "{976C4F84-5EF1-4549-BC2C-4F5E946D36E9}"
+Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "GUI", "GUI\GUI.csproj", "{976C4F84-5EF1-4549-BC2C-4F5E946D36E9}"
 EndProject
-Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "CMD", "CMD\CMD.csproj", "{6020A640-2854-41EC-BC90-73D6A0C1F74D}"
+Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "CMD", "CMD\CMD.csproj", "{6020A640-2854-41EC-BC90-73D6A0C1F74D}"
 EndProject
-Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "Test", "Test\Test.csproj", "{E59D0D0F-EEC9-48AA-8DBF-F488CF0B5FA4}"
+Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "Test", "Test\Test.csproj", "{E59D0D0F-EEC9-48AA-8DBF-F488CF0B5FA4}"
 EndProject
-Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "Util", "Util\Util.csproj", "{2C3A8087-6AFB-4EED-BF7E-93E872C699A5}"
+Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "Util", "Util\Util.csproj", "{2C3A8087-6AFB-4EED-BF7E-93E872C699A5}"
 EndProject
 Global
 	GlobalSection(SolutionConfigurationPlatforms) = preSolution

diff --git a/GUI/GUI.csproj b/GUI/GUI.csproj
@@ -12,12 +12,13 @@
     <GenerateAssemblyVersionAttribute>false</GenerateAssemblyVersionAttribute>
     <GenerateAssemblyFileVersionAttribute>false</GenerateAssemblyFileVersionAttribute>
     <ApplicationIcon>FlashLFQ_Icon.ico</ApplicationIcon>
+    <Platforms>AnyCPU</Platforms>
   </PropertyGroup>
 
   <ItemGroup>
-    <PackageReference Include="MathNet.Numerics" Version="4.9.0" />
-    <PackageReference Include="mzLib" Version="1.0.529" />
-    <PackageReference Include="NetSerializer" Version="4.1.1" />
+    <PackageReference Include="MathNet.Numerics" Version="5.0.0" />
+    <PackageReference Include="mzLib" Version="1.0.535" />
+    <PackageReference Include="NetSerializer" Version="4.1.2" />
     <PackageReference Include="Nett" Version="0.15.0" />
     <PackageReference Include="SharpLearning.Common.Interfaces" Version="0.28.0" />
     <PackageReference Include="SharpLearning.Containers" Version="0.28.0" />

diff --git a/Test/Test.cs b/Test/Test.cs
@@ -184,7 +184,7 @@ public static void TestPercolatorOutput()
                 "5"
             };
 
-            CMD.FlashLfqExecutable.Main(myargs);
+            FlashLfqExecutable.Main(myargs);
 
             string peaksPath = Path.Combine(myDirectory, "QuantifiedPeaks.tsv");
             Assert.That(File.Exists(peaksPath));
@@ -214,7 +214,7 @@ public void TestPercolatorReadPsmsGetsRTsFromFileHeader()
 
             SpectraFileInfo sfi = new SpectraFileInfo(pathOfMzml, "A", 1, 1, 1);
 
-            List<double> expectedRetentionTimes = new List<double> { 7.54, 7.54, 7.56, 7.58, 7.61, 7.63 };
+            List<double> expectedRetentionTimes = new() { 7.54, 7.54, 7.56, 7.58, 7.61, 7.63 };
 
             List<Identification> ids = PsmReader.ReadPsms(pathOfIdentificationFile, true, new List<SpectraFileInfo> { sfi });
             Assert.AreEqual(6, ids.Count);
@@ -234,7 +234,7 @@ public void TestPercolatorReadPsmsGetsRTsFromFileHeader()
             }
             CollectionAssert.AreEquivalent(expectedRetentionTimes, actualRetentionTimes);
 
-            List<int> proteinGroupCounts = new List<int> { 11, 6, 3, 2, 15, 3 };
+            List<int> proteinGroupCounts = new() { 11, 6, 3, 2, 15, 3 };
             CollectionAssert.AreEquivalent(proteinGroupCounts, ids.Select(i => i.ProteinGroups.Count).ToList());
         }
 

diff --git a/Test/Test.csproj b/Test/Test.csproj
@@ -10,12 +10,13 @@
     <GenerateAssemblyProductAttribute>false</GenerateAssemblyProductAttribute>
     <GenerateAssemblyVersionAttribute>false</GenerateAssemblyVersionAttribute>
     <GenerateAssemblyFileVersionAttribute>false</GenerateAssemblyFileVersionAttribute>
+    <Platforms>AnyCPU</Platforms>
   </PropertyGroup>
 
   <ItemGroup>
-    <PackageReference Include="MathNet.Numerics" Version="4.9.0" />
-    <PackageReference Include="mzLib" Version="1.0.529" />
-    <PackageReference Include="NetSerializer" Version="4.1.1" />
+    <PackageReference Include="MathNet.Numerics" Version="5.0.0" />
+    <PackageReference Include="mzLib" Version="1.0.535" />
+    <PackageReference Include="NetSerializer" Version="4.1.2" />
     <PackageReference Include="nunit" Version="3.13.3" />
     <PackageReference Include="NUnit3TestAdapter" Version="4.2.1" />
     <PackageReference Include="Microsoft.NET.Test.Sdk" Version="16.2.0" />

diff --git a/Util/OutputWriter.cs b/Util/OutputWriter.cs
@@ -1,5 +1,4 @@
 using System;
-using System.Collections.Generic;
 using System.IO;
 using System.Linq;
 using FlashLFQ;
@@ -16,7 +15,7 @@ public static void WriteOutput(string inputPath, FlashLfqResults results, bool s
                 outputPath = Path.GetDirectoryName(inputPath);
             }
 
-            string inputFileName = Path.GetFileNameWithoutExtension(inputPath);
+            string inputFileName = PeriodTolerantFilenameWithoutExtension.GetPeriodTolerantFilenameWithoutExtension(inputPath);
 
             if (!Directory.Exists(outputPath))
             {
@@ -41,7 +40,7 @@ public static void WriteErrorReport(Exception e, string inputPath, string output
                 outputPath = Path.GetDirectoryName(inputPath);
             }
 
-            string inputFileName = Path.GetFileNameWithoutExtension(inputPath);
+            string inputFileName = PeriodTolerantFilenameWithoutExtension.GetPeriodTolerantFilenameWithoutExtension(inputPath);
 
             if (!Directory.Exists(outputPath))
             {

diff --git a/Util/PsmReader.cs b/Util/PsmReader.cs
@@ -1,4 +1,5 @@
 using FlashLFQ;
+using MzLibUtil;
 using System;
 using System.Collections.Generic;
 using System.Globalization;
@@ -94,7 +95,7 @@ public static List<Identification> ReadPsms(string filepath, bool silent, List<S
                 throw new Exception("Could not interpret PSM header labels from file: " + filepath);
             }
 
-            var psmsGroupedByFile = inputPsms.GroupBy(p => Path.GetFileNameWithoutExtension(p.Split('\t')[_fileNameCol])).ToList();
+            var psmsGroupedByFile = inputPsms.GroupBy(p => PeriodTolerantFilenameWithoutExtension.GetPeriodTolerantFilenameWithoutExtension(p.Split('\t')[_fileNameCol])).ToList();
 
             foreach (var fileSpecificPsms in psmsGroupedByFile)
             {
@@ -187,7 +188,7 @@ private static Identification GetIdentification(string line, bool silent, Dictio
             }
 
             // spectrum file name
-            string fileName = Path.GetFileNameWithoutExtension(param[_fileNameCol]);
+            string fileName = PeriodTolerantFilenameWithoutExtension.GetPeriodTolerantFilenameWithoutExtension(param[_fileNameCol]);
 
             // base sequence
             string baseSequence = param[_baseSequCol];
@@ -445,7 +446,7 @@ private static Identification GetPercolatorIdentification(string line, List<Scan
 
             if (int.TryParse(param[_msmsScanCol], NumberStyles.Number, CultureInfo.InvariantCulture, out int scanNumber))
             {
-                ms2RetentionTime = scanHeaderInfo.Where(i => Path.GetFileNameWithoutExtension(i.FileNameWithoutExtension) == Path.GetFileNameWithoutExtension(fileName) && i.ScanNumber == scanNumber).FirstOrDefault().RetentionTime;
+                ms2RetentionTime = scanHeaderInfo.Where(i => PeriodTolerantFilenameWithoutExtension.GetPeriodTolerantFilenameWithoutExtension(i.FileNameWithoutExtension) == PeriodTolerantFilenameWithoutExtension.GetPeriodTolerantFilenameWithoutExtension(fileName) && i.ScanNumber == scanNumber).FirstOrDefault().RetentionTime;
             }
 
             // charge state
@@ -532,7 +533,7 @@ private static Identification GetPercolatorIdentification(string line, List<Scan
                 }
             }
 
-            if (!rawFileDictionary.TryGetValue(fileName, out SpectraFileInfo spectraFileInfoToUse))
+            if (!rawFileDictionary.TryGetValue(PeriodTolerantFilenameWithoutExtension.GetPeriodTolerantFilenameWithoutExtension(fileName), out SpectraFileInfo spectraFileInfoToUse))
             {
                 // skip PSMs for files with no spectrum data input
                 return null;

diff --git a/Util/ScanInfoRecovery.cs b/Util/ScanInfoRecovery.cs
@@ -16,7 +16,7 @@ private enum DataFileType
 
         public static List<ScanHeaderInfo> FileScanHeaderInfo(string fullFilePathWithExtension)
         {
-            string filename = Path.GetFileNameWithoutExtension(fullFilePathWithExtension);
+            string filename = PeriodTolerantFilenameWithoutExtension.GetPeriodTolerantFilenameWithoutExtension(fullFilePathWithExtension);
             List<ScanHeaderInfo> scanHeaderInfoList = new();
             switch (GetDataFileType(fullFilePathWithExtension))
             {

diff --git a/Util/Util.csproj b/Util/Util.csproj
@@ -9,13 +9,14 @@
     <GenerateAssemblyProductAttribute>false</GenerateAssemblyProductAttribute>
     <GenerateAssemblyVersionAttribute>false</GenerateAssemblyVersionAttribute>
     <GenerateAssemblyFileVersionAttribute>false</GenerateAssemblyFileVersionAttribute>
+    <Platforms>AnyCPU</Platforms>
   </PropertyGroup>
 
   <ItemGroup>
     <PackageReference Include="CommandLineParser" Version="2.7.82" />
-    <PackageReference Include="MathNet.Numerics" Version="4.9.0" />
-    <PackageReference Include="mzLib" Version="1.0.529" />
-    <PackageReference Include="NetSerializer" Version="4.1.1" />
+    <PackageReference Include="MathNet.Numerics" Version="5.0.0" />
+    <PackageReference Include="mzLib" Version="1.0.535" />
+    <PackageReference Include="NetSerializer" Version="4.1.2" />
     <PackageReference Include="Nett" Version="0.15.0" />
   </ItemGroup>