From 3db271873dae50d76f041cbb650ba85bb3c4d342 Mon Sep 17 00:00:00 2001
From: Ankur Juneja <ankurjuneja05@gmail.com>
Date: Wed, 17 Jul 2024 10:08:21 -0700
Subject: [PATCH] Issue 50773: Pressure traces without a TextId can't be used
 for QC trace metrics (#931)

---
 .../targetedms/parser/SkylineDocumentParser.java       | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/src/org/labkey/targetedms/parser/SkylineDocumentParser.java b/src/org/labkey/targetedms/parser/SkylineDocumentParser.java
index caa67ac52..a9ad813f7 100644
--- a/src/org/labkey/targetedms/parser/SkylineDocumentParser.java
+++ b/src/org/labkey/targetedms/parser/SkylineDocumentParser.java
@@ -3113,6 +3113,7 @@ 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
@@ -3144,7 +3145,14 @@ public List<SampleFileChromInfo> getSampleFileChromInfos(Map<String, SampleFile>
                     ChromatogramGroupId chromatogramGroupId = _binaryParser.getTextId(chromatogram);
                     if (chromatogramGroupId != null)
                     {
-                        info.setTextId(chromatogramGroupId.getQcTraceName());
+                        if (chromatogramGroupId.getQcTraceName() == null && chromatogram.getFlagValues().contains(ChromGroupHeaderInfo.FlagValues.extracted_qc_trace))
+                        {
+                            info.setTextId("QC Trace " + traceMetricIndex++);
+                        }
+                        else
+                        {
+                            info.setTextId(chromatogramGroupId.getQcTraceName());
+                        }
                     }
                     info.setChromatogramFormat(chromatogram.getChromatogramBinaryFormat().ordinal());
                     info.setChromatogramOffset(chromatogram.getLocationPoints());