Merge 24.11 to develop

Author: labkey-teamcity

src/org/labkey/targetedms/parser/ChromatogramGroupId.java

@@ -15,6 +15,7 @@
  */
 package org.labkey.targetedms.parser;
 
+import org.apache.commons.lang3.StringUtils;
 import org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass;
 
 import java.util.ArrayList;
@@ -30,12 +31,18 @@ public class ChromatogramGroupId
     private ChromatogramGroupId()
     {
     }
-    public ChromatogramGroupId(Target target, SpectrumFilter spectrumFilter)
+    public ChromatogramGroupId(Target target, String qcTraceName, SpectrumFilter spectrumFilter)
     {
         _target = target;
+        _qcTraceName = StringUtils.isEmpty(qcTraceName) ? null : qcTraceName;
         _spectrumFilter = spectrumFilter;
     }
 
+    public ChromatogramGroupId(Target target, SpectrumFilter spectrumFilter)
+    {
+        this(target, null, spectrumFilter);
+    }
+
     public Target getTarget()
     {
         return _target;
@@ -70,7 +77,7 @@ public static List<ChromatogramGroupId> fromProtos(ChromatogramGroupDataOuterCla
         {
             targets.add(new Target(target));
         }
-        for (ChromatogramGroupDataOuterClass.ChromatogramGroupIdsProto.SpectrumFilter spectrumFilter : proto.getFiltersList()) 
+        for (ChromatogramGroupDataOuterClass.ChromatogramGroupIdsProto.SpectrumFilter spectrumFilter : proto.getFiltersList())
         {
             filterClauses.add(SpectrumFilter.FilterClause.fromProtocolMessage(spectrumFilter));
         }
@@ -80,7 +87,7 @@ public static List<ChromatogramGroupId> fromProtos(ChromatogramGroupDataOuterCla
             SpectrumFilter spectrumFilter = SpectrumFilter.fromFilterClauses(
                     chromatogramGroupId.getFilterIndexesList().stream()
                     .map(filterClauses::get).collect(Collectors.toList())).orElse(null);
-            list.add(new ChromatogramGroupId(targets.get(chromatogramGroupId.getTargetIndex()), spectrumFilter));
+            list.add(new ChromatogramGroupId(targets.get(chromatogramGroupId.getTargetIndex()), chromatogramGroupId.getQcTraceName(), spectrumFilter));
         }
         return list;
     }

src/org/labkey/targetedms/parser/SkylineDocumentParser.java

@@ -3126,7 +3126,6 @@ public List<SampleFileChromInfo> getSampleFileChromInfos(Map<String, SampleFile>
         {
             return Collections.emptyList();
         }
-        int traceMetricIndex = 1;
         for (ChromGroupHeaderInfo chromatogram : _binaryParser.getChromatograms())
         {
             // Sample-scoped chromatograms have a magic precursor MZ value
@@ -3158,14 +3157,7 @@ public List<SampleFileChromInfo> getSampleFileChromInfos(Map<String, SampleFile>
                     ChromatogramGroupId chromatogramGroupId = _binaryParser.getTextId(chromatogram);
                     if (chromatogramGroupId != null)
                     {
-                        if (chromatogramGroupId.getQcTraceName() == null && chromatogram.getFlagValues().contains(ChromGroupHeaderInfo.FlagValues.extracted_qc_trace))
-                        {
-                            info.setTextId("QC Trace " + traceMetricIndex++);
-                        }
-                        else
-                        {
-                            info.setTextId(chromatogramGroupId.getQcTraceName());
-                        }
+                        info.setTextId(chromatogramGroupId.getQcTraceName());
                     }
                     info.setChromatogramFormat(chromatogram.getChromatogramBinaryFormat().ordinal());
                     info.setChromatogramOffset(chromatogram.getLocationPoints());