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Issue 50773: Pressure traces without a TextId can't be used for QC trace metrics #931

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merged 1 commit into from
Jul 17, 2024
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Issue 50773: Pressure traces without a TextId can't be used for QC trace metrics #931

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10 changes: 9 additions & 1 deletion src/org/labkey/targetedms/parser/SkylineDocumentParser.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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());
Expand Down