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Fix GC-MS Fiehn RI Console compatibility #779

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Merged
YukiMatsuzawa merged 1 commit into from
Sep 2, 2026
Merged

Fix GC-MS Fiehn RI Console compatibility #779

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116 changes: 92 additions & 24 deletions tests/MSDIAL5/MsdialCoreTestApp/Parser/ConfigParser.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,7 @@ private ConfigParser() { }
public static MsdialGcmsParameter ReadForGcms(string filepath)
{
var param = new MsdialGcmsParameter();
using (var sr = new StreamReader(filepath, Encoding.ASCII))
using (var sr = new StreamReader(filepath, Encoding.UTF8, detectEncodingFromByteOrderMarks: true))
{
while (sr.Peek() > -1)
{
Expand All @@ -44,6 +44,7 @@ public static MsdialGcmsParameter ReadForGcms(string filepath)
param.MassSliceWidth = 0.5F;
param.CentroidMs1Tolerance = 0.5F;
}
ResolveGcmsFilePaths(param, filepath);

return param;
}
Expand Down Expand Up @@ -416,38 +417,83 @@ private static void readFieldValues(string? line, out string method, out string
method = string.Empty; value = string.Empty; isReadable = false;
if (string.IsNullOrEmpty(line)) return;
if (line!.Length < 2) return;
if (line[0] == '#') return;

var lineArray = line.Split(':');
if (lineArray.Length < 2) return;
method = lineArray[0].Trim();
value = line.Substring(line.Split(':')[0].Length + 1).Trim();
if (line.TrimStart().StartsWith("#", StringComparison.Ordinal)) return;

var colonIndex = line.IndexOf(':');
var equalsIndex = line.IndexOf('=');
var separatorIndex = colonIndex < 0
? equalsIndex
: equalsIndex < 0
? colonIndex
: Math.Min(colonIndex, equalsIndex);
if (separatorIndex < 0) return;

method = line.Substring(0, separatorIndex).Trim();
value = line.Substring(separatorIndex + 1).Trim();
if (value.Length >= 2
&& ((value[0] == '"' && value[value.Length - 1] == '"')
|| (value[0] == '\'' && value[value.Length - 1] == '\''))) {
value = value.Substring(1, value.Length - 2).Trim();
}
isReadable = true;
}

private static void ResolveGcmsFilePaths(MsdialGcmsParameter param, string methodFilePath) {
param.MspFilePath = ResolvePathFromMethodFile(param.MspFilePath, methodFilePath);
param.LbmFilePath = ResolvePathFromMethodFile(param.LbmFilePath, methodFilePath);
param.TextDBFilePath = ResolvePathFromMethodFile(param.TextDBFilePath, methodFilePath);
param.IsotopeTextDBFilePath = ResolvePathFromMethodFile(param.IsotopeTextDBFilePath, methodFilePath);
param.CompoundListInTargetModePath = ResolvePathFromMethodFile(param.CompoundListInTargetModePath, methodFilePath);
param.CompoundListForRtCorrectionPath = ResolvePathFromMethodFile(param.CompoundListForRtCorrectionPath, methodFilePath);
param.ReferenceFileParam.RtCorrectionPeakSelectionFilePath = ResolvePathFromMethodFile(param.ReferenceFileParam.RtCorrectionPeakSelectionFilePath, methodFilePath);
param.RiDictionaryFilePath = ResolvePathFromMethodFile(param.RiDictionaryFilePath, methodFilePath);
}

private static string ResolvePathFromMethodFile(string? path, string methodFilePath) {
if (path.IsEmptyOrNull()) {
return string.Empty;
}

var expanded = Environment.ExpandEnvironmentVariables(path!.Trim());
if (Path.IsPathRooted(expanded)) {
return Path.GetFullPath(expanded);
}

var methodDirectory = Path.GetDirectoryName(Path.GetFullPath(methodFilePath)) ?? Environment.CurrentDirectory;
return Path.GetFullPath(Path.Combine(methodDirectory, expanded));
}

public static bool ReadGcmsSpecificParameter(MsdialGcmsParameter param, string method, string value) {
if (value.IsEmptyOrNull()) return false;
if (method.IsEmptyOrNull()) return false;
method = method.ToLower();
value = value.ToLower();
var valueLower = value.ToLower();
switch (method) {
case "ri index file pathes": param.RiDictionaryFilePath = value; return true;
case "ri index file pathes":
case "ri index file paths":
case "ri dictionary file path":
case "ri dictionary file paths":
param.RiDictionaryFilePath = value;
return true;
case "retention type":
if (value == "rt" || value == "ri")
param.RetentionType = (RetentionType)Enum.Parse(typeof(RetentionType), value, true);
if (valueLower == "rt" || valueLower == "ri")
param.RetentionType = (RetentionType)Enum.Parse(typeof(RetentionType), valueLower, true);
return true;
case "ri compound":
case "ri compound type":
if (value == "fames" || value == "alkanes")
param.RiCompoundType = (RiCompoundType)Enum.Parse(typeof(RiCompoundType), value, true);
if (valueLower == "fames" || valueLower == "alkanes")
param.RiCompoundType = (RiCompoundType)Enum.Parse(typeof(RiCompoundType), valueLower, true);
return true;
case "alignment index type": if (valueLower == "ri") param.AlignmentIndexType = AlignmentIndexType.RI; else param.AlignmentIndexType = AlignmentIndexType.RT; return true;
case "retention index tolerance for alignment":
case "retention index alignment tolerance":
if (float.TryParse(valueLower, out float ritol_align)) param.RetentionIndexAlignmentTolerance = ritol_align;
return true;
case "alignment index type": if (value == "ri") param.AlignmentIndexType = AlignmentIndexType.RI; else param.AlignmentIndexType = AlignmentIndexType.RT; return true;
case "retention index tolerance for alignment": if (float.TryParse(value, out float ritol_align)) param.RetentionIndexAlignmentTolerance = ritol_align; return true;
case "replace quant mass by user defined value":
if (value == "true")
if (valueLower == "true")
param.IsReplaceQuantmassByUserDefinedValue = true; return true;
case "is quant mass based on base peak mz":
if (value == "true")
if (valueLower == "true")
param.IsRepresentativeQuantMassBasedOnBasePeakMz = true; return true;
default: return false;
}
Expand Down Expand Up @@ -682,7 +728,11 @@ public static bool ReadCommonParameter(ParameterBase param, string method, strin

//Identification
case "rt tolerance for msp-based annotation": if (float.TryParse(valueLower, out float rttol_ident)) param.MspSearchParam.RtTolerance = rttol_ident; return true;
case "ri tolerance for msp-based annotation": if (float.TryParse(valueLower, out float ritol_ident)) param.MspSearchParam.RiTolerance = ritol_ident; return true;
case "ri tolerance for msp-based annotation":
case "ri tolerance for identification":
case "retention index tolerance for identification":
if (float.TryParse(valueLower, out float ritol_ident)) param.MspSearchParam.RiTolerance = ritol_ident;
return true;
case "ccs tolerance for msp-based annotation": if (float.TryParse(valueLower, out float ccstol_ident)) param.MspSearchParam.CcsTolerance = ccstol_ident; return true;
case "mass range begin for msp-based annotation": if (float.TryParse(valueLower, out float msbegin_ident)) param.MspSearchParam.MassRangeBegin = msbegin_ident; return true;
case "mass range end for msp-based annotation": if (float.TryParse(valueLower, out float msend_ident)) param.MspSearchParam.MassRangeEnd = msend_ident; return true;
Expand All @@ -691,11 +741,26 @@ public static bool ReadCommonParameter(ParameterBase param, string method, strin
case "weighted dot product cutoff for msp-based annotation": if (float.TryParse(valueLower, out float sqdotproduct)) param.MspSearchParam.SquaredWeightedDotProductCutOff = sqdotproduct; return true;
case "simple dot product cutoff for msp-based annotation": if (float.TryParse(valueLower, out float sqsimpleproduct)) param.MspSearchParam.SquaredSimpleDotProductCutOff = sqsimpleproduct; return true;
case "reverse dot product cutoff for msp-based annotation": if (float.TryParse(valueLower, out float sqrevdotproduct)) param.MspSearchParam.SquaredReverseDotProductCutOff = sqrevdotproduct; return true;
case "square root of weighted dot product cutoff for msp-based annotation": if (float.TryParse(valueLower, out float dotproduct)) param.MspSearchParam.WeightedDotProductCutOff = dotproduct; return true;
case "square root of simple dot product cutoff for msp-based annotation": if (float.TryParse(valueLower, out float simpleproduct)) param.MspSearchParam.SimpleDotProductCutOff = simpleproduct; return true;
case "square root of reverse dot product cutoff for msp-based annotation": if (float.TryParse(valueLower, out float revdotproduct)) param.MspSearchParam.ReverseDotProductCutOff = revdotproduct; return true;
case "matched peaks percentage cutoff for msp-based annotation": if (float.TryParse(valueLower, out float matchedpeakspercent)) param.MspSearchParam.MatchedPeaksPercentageCutOff = matchedpeakspercent; return true;
case "minimum spectrum match for msp-based annotation": if (float.TryParse(valueLower, out float minpeakmatch)) param.MspSearchParam.MinimumSpectrumMatch = minpeakmatch; return true;
case "weighted dot product cutoff":
case "square root of weighted dot product cutoff for msp-based annotation":
if (float.TryParse(valueLower, out float dotproduct)) param.MspSearchParam.WeightedDotProductCutOff = dotproduct;
return true;
case "simple dot product cutoff":
case "square root of simple dot product cutoff for msp-based annotation":
if (float.TryParse(valueLower, out float simpleproduct)) param.MspSearchParam.SimpleDotProductCutOff = simpleproduct;
return true;
case "reverse dot product cutoff":
case "square root of reverse dot product cutoff for msp-based annotation":
if (float.TryParse(valueLower, out float revdotproduct)) param.MspSearchParam.ReverseDotProductCutOff = revdotproduct;
return true;
case "matched peaks percentage cutoff":
case "matched peaks percentage cutoff for msp-based annotation":
if (float.TryParse(valueLower, out float matchedpeakspercent)) param.MspSearchParam.MatchedPeaksPercentageCutOff = matchedpeakspercent;
return true;
case "minimum spectrum match":
case "minimum spectrum match for msp-based annotation":
if (float.TryParse(valueLower, out float minpeakmatch)) param.MspSearchParam.MinimumSpectrumMatch = minpeakmatch;
return true;
case "total score cutoff for msp-based annotation": if (float.TryParse(valueLower, out float cutoff_ident)) param.MspSearchParam.TotalScoreCutoff = cutoff_ident; return true;
case "ms1 tolerance for msp-based annotation": if (float.TryParse(valueLower, out float ms1tol_ident)) param.MspSearchParam.Ms1Tolerance = ms1tol_ident; return true;
case "ms2 tolerance for msp-based annotation": if (float.TryParse(valueLower, out float ms2tol_ident)) param.MspSearchParam.Ms2Tolerance = ms2tol_ident; return true;
Expand All @@ -704,7 +769,10 @@ public static bool ReadCommonParameter(ParameterBase param, string method, strin
case "use ccs for msp-based annotation scoring": if (valueLower == "true" || valueLower == "false") param.MspSearchParam.IsUseCcsForAnnotationScoring = bool.Parse(valueLower); return true;
case "use ccs for msp-based annotation filtering": if (valueLower == "true" || valueLower == "false") param.MspSearchParam.IsUseCcsForAnnotationFiltering = bool.Parse(valueLower); return true;
case "only report top hit for msp-based annotation": if (valueLower == "true" || valueLower == "false") param.OnlyReportTopHitInMspSearch = bool.Parse(valueLower); return true;
case "execute annotation process only for alignment file for msp-based annotation": if (valueLower == "true" || valueLower == "false") param.IsIdentificationOnlyPerformedForAlignmentFile = bool.Parse(valueLower); return true;
case "execute annotation process only for alignment file":
case "execute annotation process only for alignment file for msp-based annotation":
if (valueLower == "true" || valueLower == "false") param.IsIdentificationOnlyPerformedForAlignmentFile = bool.Parse(valueLower);
return true;

//Identification
case "rt tolerance for lbm-based annotation": if (float.TryParse(valueLower, out float rttol_lbm_ident)) param.LbmSearchParam.RtTolerance = rttol_lbm_ident; return true;
Expand Down
50 changes: 45 additions & 5 deletions tests/MSDIAL5/MsdialCoreTestApp/Process/GcmsProcess.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -41,14 +41,21 @@ public int Run(string inputFolder, string outputFolder, string methodFile, bool
return -1;
}

if (!param.MspFilePath.IsEmptyOrNull() && !File.Exists(param.MspFilePath)) {
throw new FileNotFoundException(
$"The GC-MS MSP reference library was not found. Parsed path: '{param.MspFilePath}'. "
+ "Check the 'Msp file path' entry in the method file.",
param.MspFilePath);
}

if (param.RiDictionaryFilePath != string.Empty)
{
if (!File.Exists(param.RiDictionaryFilePath)) {
throw new FileNotFoundException(string.Format("File '{0}' does not exist.", param.RiDictionaryFilePath));
}

if (!CheckRiDicionaryFiles(analysisFiles, param.RiDictionaryFilePath, out var errorMessage)) {
throw new FileNotFoundException(string.Format(errorMessage, param.RiDictionaryFilePath));
throw new FileNotFoundException(errorMessage, param.RiDictionaryFilePath);
}

//probably, at least in fiehn lab, this has to be automatically set from GCMS raw data.
Expand Down Expand Up @@ -79,11 +86,27 @@ public int Run(string inputFolder, string outputFolder, string methodFile, bool
}
}

Console.WriteLine(
$"GC-MS retention matching: {param.RetentionType}; RI compound type: {param.RiCompoundType}; "
+ $"RI dictionaries: {param.FileIdRiInfoDictionary?.Count ?? 0}");

CommonProcess.ParseLibraries(param, -1, out IupacDatabase iupacDB,
out var mspDB, out var txtDB,
out List<MoleculeMsReference> isotopeTextDB, out List<MoleculeMsReference> compoundsInTargetMode,
out var lbmDB);

if (!param.MspFilePath.IsEmptyOrNull() && (mspDB is null || mspDB.Database.Count == 0)) {
throw new InvalidDataException(
$"The GC-MS MSP reference library contained no readable records: '{param.MspFilePath}'. "
+ "Check that the file is a valid MSP library.");
}
if (mspDB is { Database.Count: > 0 }) {
Console.WriteLine($"GC-MS MSP reference library: {param.MspFilePath} ({mspDB.Database.Count} records)");
}
else {
Console.WriteLine("GC-MS reference matching is disabled because 'Msp file path' is empty.");
}


var container = new MsdialGcmsDataStorage()
{
Expand Down Expand Up @@ -145,18 +168,19 @@ private bool IsFamesContanesMatch(Dictionary<int, float>? riDictionary)
private bool CheckRiDicionaryFiles(List<AnalysisFileBean> analysisFiles, string riDictionaryFile, out string errorMessage)
{
errorMessage = string.Empty;
using (var sr = new StreamReader(riDictionaryFile, Encoding.ASCII)) {
var mappingDirectory = Path.GetDirectoryName(Path.GetFullPath(riDictionaryFile)) ?? Environment.CurrentDirectory;
using (var sr = new StreamReader(riDictionaryFile, Encoding.UTF8, detectEncodingFromByteOrderMarks: true)) {
while (sr.Peek() > -1) {
var line = sr.ReadLine();
if (string.IsNullOrEmpty(line)) continue;
var lineArray = line.Split('\t');
if (lineArray.Length < 2) continue;

var analysisFilePath = lineArray[0];
var riFilePath = lineArray[1];
var analysisFilePath = ResolveMappingPath(lineArray[0], mappingDirectory);
var riFilePath = ResolveMappingPath(lineArray[1], mappingDirectory);

foreach (var file in analysisFiles) {
if (file.AnalysisFilePath == analysisFilePath) {
if (IsSamePath(file.AnalysisFilePath, analysisFilePath)) {
file.RiDictionaryFilePath = riFilePath;
break;
}
Expand All @@ -179,6 +203,22 @@ private bool CheckRiDicionaryFiles(List<AnalysisFileBean> analysisFiles, string
}
}

private static string ResolveMappingPath(string path, string mappingDirectory)
{
var normalized = path.Trim().Trim('"', '\'');
return Path.GetFullPath(Path.IsPathRooted(normalized)
? normalized
: Path.Combine(mappingDirectory, normalized));
}

private static bool IsSamePath(string first, string second)
{
var comparison = Path.DirectorySeparatorChar == '\\'
? StringComparison.OrdinalIgnoreCase
: StringComparison.Ordinal;
return string.Equals(Path.GetFullPath(first), Path.GetFullPath(second), comparison);
}

private async Task<int> ExecuteAsync(MsdialGcmsDataStorage storage, string outputFolder, bool isProjectSaved) {
var projectDataStorage = new ProjectDataStorage(new ProjectParameter(DateTime.Now, storage.MsdialGcmsParameter.ProjectParam.ProjectFolderPath, Path.ChangeExtension(storage.MsdialGcmsParameter.ProjectParam.ProjectFileName, ".mdproject")));
projectDataStorage.AddStorage(storage);
Expand Down
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