Fix MS-DIAL Console lcimms crash in alignment export (drift spots had no deconvolution result)

tests/MSDIAL5/MsdialCoreTestApp/Process/LcimmsProcess.cs

@@ -137,7 +137,7 @@ private async Task<int> ExecuteAsync(IMsdialDataStorage<MsdialLcImMsParameter> s
             aligner.ProviderFactory = providerFactory;
             var result = aligner.Alignment(files, alignmentFile, serializer);
             result.Save(alignmentFile);
-            var align_decResults = LoadRepresentativeDeconvolutions(storage, result.AlignmentSpotProperties).ToList();
+            var align_decResults = LoadRepresentativeDeconvolutions(files, result.AlignmentSpotProperties).ToList();
             MsdecResultsWriter.Write(alignmentFile.SpectraFilePath, align_decResults);
 
             var align_accessor = new LcimmsMetadataAccessor(storage.DataBaseMapper, storage.Parameter, false);
@@ -184,29 +184,20 @@ private async Task<int> ExecuteAsync(IMsdialDataStorage<MsdialLcImMsParameter> s
         return 0;
     }
 
-    private static IEnumerable<MSDecResult> LoadRepresentativeDeconvolutions(IMsdialDataStorage<MsdialLcImMsParameter> storage, IReadOnlyList<AlignmentSpotProperty> spots) {
-        var files = storage.AnalysisFiles;
-
-        var pointerss = new List<(int version, List<long> pointers, bool isAnnotationInfo)>();
-        foreach (var file in files) {
-            MsdecResultsReader.GetSeekPointers(file.DeconvolutionFilePath, out var version, out var pointers, out var isAnnotationInfo);
-            pointerss.Add((version, pointers, isAnnotationInfo));
-        }
-
-        var streams = new List<FileStream>();
-        try {
-            streams = files.Select(file => File.OpenRead(file.DeconvolutionFilePath)).ToList();
-            foreach (var spot in spots.OrEmptyIfNull()) {
-                var repID = spot.RepresentativeFileID;
-                var peakID = spot.AlignedPeakProperties[repID].MasterPeakID;
-                var decResult = MsdecResultsReader.ReadMSDecResult(
-                    streams[repID], pointerss[repID].pointers[peakID],
-                    pointerss[repID].version, pointerss[repID].isAnnotationInfo);
-                yield return decResult;
+    /// <summary>
+    /// One deconvolution result per alignment spot, indexed by MasterAlignmentID: each RT spot followed by its
+    /// drift spots, the order LcimmsAlignmentRefiner numbers them in and the GUI's
+    /// AlignmentFileBeanModel.LoadMSDecResultsFromEachFiles reads them in. AlignmentCSVExporter and
+    /// MztabFormatExporter index this list by the drift spots' MasterAlignmentID too, so a list of the RT
+    /// spots alone overflowed on the first drift spot.
+    /// </summary>
+    internal static IEnumerable<MSDecResult> LoadRepresentativeDeconvolutions(IReadOnlyList<AnalysisFileBean> files, IReadOnlyList<AlignmentSpotProperty>? spots) {
+        using var reader = new RepresentativeDeconvolutionReader(files);
+        foreach (var spot in spots.OrEmptyIfNull()) {
+            yield return reader.Read(spot.AlignedPeakProperties[spot.RepresentativeFileID]);
+            foreach (var driftSpot in spot.AlignmentDriftSpotFeatures.OrEmptyIfNull()) {
+                yield return reader.Read(driftSpot.AlignedPeakProperties[driftSpot.RepresentativeFileID]);
             }
         }
-        finally {
-            streams.ForEach(stream => stream.Close());
-        }
     }
 }

tests/MSDIAL5/MsdialCoreTestAppTests/Process/LcimmsProcessTests.cs

@@ -0,0 +1,82 @@
+using CompMs.App.MsdialConsole.Process;
+using CompMs.MsdialCore.DataObj;
+using CompMs.MsdialCore.MSDec;
+using CompMs.MsdialCore.Parser;
+using Microsoft.VisualStudio.TestTools.UnitTesting;
+using System;
+using System.Collections.Generic;
+using System.IO;
+using System.Linq;
+
+namespace MsdialCoreTestAppTests.Process;
+
+/// <summary>
+/// The LC-IM-MS alignment export indexes the deconvolution results by MasterAlignmentID for the drift spots as
+/// well as the RT spots. The Console loaded one result per RT spot only, so AlignmentCSVExporter.Export threw
+/// ArgumentOutOfRangeException on the first drift spot.
+/// </summary>
+[TestClass]
+public sealed class LcimmsProcessTests
+{
+    private string _scratch = null!;
+
+    [TestInitialize]
+    public void Initialize() {
+        _scratch = Path.Combine(Path.GetTempPath(), $"msdial-lcimms-dcl-{Guid.NewGuid():N}");
+        Directory.CreateDirectory(_scratch);
+    }
+
+    [TestCleanup]
+    public void Cleanup() {
+        if (Directory.Exists(_scratch)) {
+            Directory.Delete(_scratch, recursive: true);
+        }
+    }
+
+    [TestMethod]
+    public void EveryRtAndDriftSpotHasItsResultAtItsMasterAlignmentId() {
+        var file0 = NewFile(0, "file0", peakCount: 6);
+        var file1 = NewFile(1, "file1", peakCount: 6);
+        // Numbered as LcimmsAlignmentRefiner numbers them: each RT spot, then its drift spots.
+        var spots = new List<AlignmentSpotProperty>
+        {
+            Spot(0, representative: 0, masterPeakId: 0, Spot(1, representative: 1, masterPeakId: 1), Spot(2, representative: 0, masterPeakId: 2)),
+            Spot(3, representative: 1, masterPeakId: 3),
+            Spot(4, representative: 1, masterPeakId: 4, Spot(5, representative: 0, masterPeakId: 5)),
+        };
+
+        var results = LcimmsProcess.LoadRepresentativeDeconvolutions([file0, file1], spots).ToList();
+
+        Assert.AreEqual(6, results.Count);
+        foreach (var spot in spots.SelectMany(s => s.AlignmentDriftSpotFeatures.Prepend(s))) {
+            var peak = spot.AlignedPeakProperties[spot.RepresentativeFileID];
+            Assert.AreEqual(Marker(peak.FileID, peak.MasterPeakID), results[spot.MasterAlignmentID].PrecursorMz, $"spot {spot.MasterAlignmentID}");
+        }
+    }
+
+    private AnalysisFileBean NewFile(int id, string name, int peakCount) {
+        var file = new AnalysisFileBean {
+            AnalysisFileId = id,
+            AnalysisFileName = name,
+            AnalysisFilePath = Path.Combine(_scratch, name + ".d"),
+            DeconvolutionFilePath = Path.Combine(_scratch, name + "_202610181.dcl"),
+        };
+        var results = Enumerable.Range(0, peakCount).Select(i => new MSDecResult { ScanID = i, PrecursorMz = Marker(id, i), }).ToList();
+        MsdecResultsWriter.Write(file.DeconvolutionFilePath, results);
+        return file;
+    }
+
+    private static AlignmentSpotProperty Spot(int masterAlignmentId, int representative, int masterPeakId, params AlignmentSpotProperty[] driftSpots) {
+        return new AlignmentSpotProperty {
+            MasterAlignmentID = masterAlignmentId,
+            RepresentativeFileID = representative,
+            AlignedPeakProperties = Enumerable.Range(0, 2)
+                .Select(fileId => new AlignmentChromPeakFeature { FileID = fileId, MasterPeakID = fileId == representative ? masterPeakId : -1, })
+                .ToList(),
+            AlignmentDriftSpotFeatures = driftSpots.ToList(),
+        };
+    }
+
+    // Which file and which peak a result came from.
+    private static double Marker(int fileId, int peak) => fileId * 1000d + peak;
+}