[bot] Fast-forward for 26.3.8

src/org/labkey/targetedms/TargetedMSController.java

@@ -874,6 +874,7 @@ public static class LeveyJenningsPlotOptions
         private Integer _trailingRuns;
         private Integer _calendarMonthsToShow;
         private String _heatmapDataSource;
+        private String _hiddenSeries;
 
         public Map<String, String> getAsMapOfStrings()
         {
@@ -906,6 +907,8 @@ public Map<String, String> getAsMapOfStrings()
                 valueMap.put("calendarMonthsToShow", Integer.toString(_calendarMonthsToShow));
             if (_heatmapDataSource != null)
                 valueMap.put("heatMapDataSource", _heatmapDataSource);
+            if (_hiddenSeries != null)
+                valueMap.put("hiddenSeries", _hiddenSeries);
             // note: start and end date handled separately since they can be null and we want to persist that
             return valueMap;
         }
@@ -1034,6 +1037,16 @@ public void setHeatmapDataSource(String heatmapDataSource)
         {
             _heatmapDataSource = heatmapDataSource;
         }
+
+        public String getHiddenSeries()
+        {
+            return _hiddenSeries;
+        }
+
+        public void setHiddenSeries(String hiddenSeries)
+        {
+            _hiddenSeries = hiddenSeries;
+        }
     }
 
     @RequiresPermission(ReadPermission.class)

src/org/labkey/targetedms/model/QCPlotFragment.java

@@ -21,6 +21,12 @@ public class QCPlotFragment
     private List<GuideSetStats> guideSetStats;
     @Nullable
     private Color _seriesColor;
+    @Nullable
+    private Long precursorRowId;
+    @Nullable
+    private Long peptideGroupId;
+    @Nullable
+    private String peptideGroupLabel;
 
     public String getSeriesLabel()
     {
@@ -77,6 +83,11 @@ public JSONObject toJSON(boolean includeLJ, boolean includeMR, boolean includeMe
         JSONObject jsonObject = new JSONObject();
         jsonObject.put("DataType", getDataType());
         jsonObject.put("SeriesLabel", getSeriesLabel());
+        if (peptideGroupId != null)
+        {
+            jsonObject.put("PeptideGroupId", peptideGroupId);
+            jsonObject.put("PeptideGroupLabel", peptideGroupLabel != null ? peptideGroupLabel : "");
+        }
         if (_seriesColor != null)
         {
             jsonObject.put("SeriesColor", "#" + Integer.toHexString(_seriesColor.getRGB()).substring(2).toUpperCase());
@@ -205,4 +216,37 @@ public Color getSeriesColor()
     {
         return _seriesColor;
     }
+
+    @Nullable
+    public Long getPrecursorRowId()
+    {
+        return precursorRowId;
+    }
+
+    public void setPrecursorRowId(Long precursorRowId)
+    {
+        this.precursorRowId = precursorRowId;
+    }
+
+    @Nullable
+    public Long getPeptideGroupId()
+    {
+        return peptideGroupId;
+    }
+
+    public void setPeptideGroupId(Long peptideGroupId)
+    {
+        this.peptideGroupId = peptideGroupId;
+    }
+
+    @Nullable
+    public String getPeptideGroupLabel()
+    {
+        return peptideGroupLabel;
+    }
+
+    public void setPeptideGroupLabel(String peptideGroupLabel)
+    {
+        this.peptideGroupLabel = peptideGroupLabel;
+    }
 }

src/org/labkey/targetedms/outliers/OutlierGenerator.java

@@ -44,9 +44,11 @@
 import org.labkey.targetedms.model.SampleFileQCMetadata;
 import org.labkey.targetedms.parser.GeneralMolecule;
 import org.labkey.targetedms.parser.GeneralPrecursor;
+import org.labkey.targetedms.parser.PeptideGroup;
 import org.labkey.targetedms.parser.SampleFile;
 import org.labkey.targetedms.query.MoleculeManager;
 import org.labkey.targetedms.query.MoleculePrecursorManager;
+import org.labkey.targetedms.query.PeptideGroupManager;
 import org.labkey.targetedms.query.PeptideManager;
 import org.labkey.targetedms.query.PrecursorManager;
 
@@ -539,7 +541,11 @@ public List<QCPlotFragment> getQCPlotFragment(List<RawMetricDataSet> rawMetricDa
             Optional<RawMetricDataSet> bestPrecursorIdRow = entry.getValue().stream().filter(x -> x.getPrecursorId() != null).min(Comparator.comparing(RawMetricDataSet::getPrecursorId));
 
             // Remember the precursor ID so that we can assign a series color based on Skyline's algorithm
-            bestPrecursorIdRow.ifPresent(rawMetricDataSet -> fragmentsByPrecursorId.put(rawMetricDataSet.getPrecursorId(), qcPlotFragment));
+            // and to sort by Skyline document order (row ID) instead of alphabetically
+            bestPrecursorIdRow.ifPresent(rawMetricDataSet -> {
+                fragmentsByPrecursorId.put(rawMetricDataSet.getPrecursorId(), qcPlotFragment);
+                qcPlotFragment.setPrecursorRowId(rawMetricDataSet.getPrecursorId());
+            });
 
             qcPlotFragment.setSeriesLabel(entry.getKey());
             qcPlotFragment.setQcPlotData(entry.getValue());
@@ -559,6 +565,7 @@ public List<QCPlotFragment> getQCPlotFragment(List<RawMetricDataSet> rawMetricDa
         // Now that we have all the precursor IDs, in order (important so that we de-dupe the colors in a stable order),
         // run through them and choose a color
         Set<Color> seriesColors = new HashSet<>();
+        Map<Long, PeptideGroup> peptideGroupCache = new HashMap<>();
         for (Map.Entry<Long, QCPlotFragment> entry : fragmentsByPrecursorId.entrySet())
         {
             long precursorId = entry.getKey();
@@ -588,10 +595,21 @@ public List<QCPlotFragment> getQCPlotFragment(List<RawMetricDataSet> rawMetricDa
                 Color color = ColorGenerator.getColor(molecule.getTextId(), seriesColors);
                 entry.getValue().setSeriesColor(color);
                 seriesColors.add(color);
+
+                // set the peptide group (protein / molecule list) for the combined plot tree legend
+                PeptideGroup peptideGroup = peptideGroupCache.computeIfAbsent(molecule.getPeptideGroupId(), id -> PeptideGroupManager.getPeptideGroup(c, id));
+                if (peptideGroup != null)
+                {
+                    entry.getValue().setPeptideGroupId(peptideGroup.getId());
+                    entry.getValue().setPeptideGroupLabel(peptideGroup.getLabel());
+                }
             }
         }
 
-        qcPlotFragments.sort(Comparator.comparing(QCPlotFragment::getSeriesLabel));
+        // Sort by precursor row ID to preserve Skyline document order. Fragments with no precursor ID
+        // (e.g. trace metrics) fall back to alphabetical order after all precursor-scoped series.
+        qcPlotFragments.sort(Comparator.comparing(QCPlotFragment::getPrecursorRowId, Comparator.nullsLast(Comparator.naturalOrder()))
+                .thenComparing(QCPlotFragment::getSeriesLabel));
         return qcPlotFragments;
     }
 

test/src/org/labkey/test/components/targetedms/QCPlotsWebPart.java

@@ -636,6 +636,20 @@ public Locator getLegendItemLocator(String text, boolean exactMatch)
             return elementCache().legendItem.containing(text);
     }
 
+    public Locator getTreeLegendItemLocator(String text, boolean exactMatch)
+    {
+        if (exactMatch)
+            return elementCache().combinedTreeLegendItem.withText(text);
+        else
+            return elementCache().combinedTreeLegendItem.containing(text);
+    }
+
+    public Locator getTreeLegendPrecursorLocator(String text)
+    {
+        // Match data-fragment attribute to avoid relying on potentially overflow-hidden span text
+        return Locator.css(".qc-tree-precursor").withAttributeContaining("data-fragment", text);
+    }
+
     public Locator getLegendItemLocatorByTitle(String text)
     {
         // Use containing instead of withText() to ignore the +2 or other suffices
@@ -933,6 +947,7 @@ public class Elements extends BodyWebPart<?>.ElementCache
         Locator.CssLocator legendItem = Locator.css("svg g.legend-item");
         Locator.CssLocator legendItemTitle = Locator.css("svg g.legend-item title");
         Locator.CssLocator legendItemPopup = Locator.css(".headerlegendpopup svg g.legend-item");
+        Locator.CssLocator combinedTreeLegendItem = Locator.css(".qc-combined-tree-legend > div");
         Locator.CssLocator paginationPrevBtn = Locator.css(".qc-paging-prev");
         Locator.CssLocator paginationNextBtn = Locator.css(".qc-paging-next");
         Locator.CssLocator svgBackgrounds = Locator.css("svg g.brush rect.background");

test/src/org/labkey/test/tests/panoramapremium/TargetedMSHidePeptidesAndMolecules.java

@@ -13,6 +13,10 @@
 
 import java.util.Arrays;
 
+/**
+ * Tests the ability to hide/show specific peptides and molecules in QC folders across multiple folder structure
+ * configurations.
+ */
 @Category({})
 @BaseWebDriverTest.ClassTimeout(minutes = 6)
 public class TargetedMSHidePeptidesAndMolecules extends TargetedMSTest

test/src/org/labkey/test/tests/panoramapremium/TargetedMSIsotopologueTest.java

@@ -13,6 +13,9 @@
 
 import static org.junit.Assert.assertTrue;
 
+/**
+ * Validates isotopologue metric display and calculation in the Panorama Dashboard QC metrics panel.
+ */
 @Category({})
 @BaseWebDriverTest.ClassTimeout(minutes = 3)
 public class TargetedMSIsotopologueTest extends TargetedMSPremiumTest

test/src/org/labkey/test/tests/panoramapremium/TargetedMSQCFolderImportExport.java

@@ -17,6 +17,9 @@
 import java.util.LinkedHashMap;
 import java.util.Map;
 
+/**
+ * Tests import/export of QC folder configurations and data as a round-trip operation.
+ */
 @Category({})
 @BaseWebDriverTest.ClassTimeout(minutes = 6)
 public class TargetedMSQCFolderImportExport extends TargetedMSPremiumTest

test/src/org/labkey/test/tests/panoramapremium/TargetedMSQCPremiumTest.java

@@ -37,6 +37,10 @@
 import static org.labkey.test.components.targetedms.QCPlotsWebPart.QCPlotType.CUSUMm;
 import static org.labkey.test.util.PermissionsHelper.READER_ROLE;
 
+/**
+ * Tests premium-tier QC functionality: guide sets, advanced QC metrics, CUSUM plots, and premium-specific permission
+ * checks.
+ */
 @Category({})
 @BaseWebDriverTest.ClassTimeout(minutes = 6)
 public class TargetedMSQCPremiumTest extends TargetedMSPremiumTest

test/src/org/labkey/test/tests/panoramapremium/TargetedMSSampleManagerIntegrationTest.java

@@ -20,6 +20,10 @@
 import java.util.List;
 import java.util.Map;
 
+/**
+ * Tests integration between TargetedMS and the Sample Manager module, including linked sample type data flowing into
+ * Skyline documents.
+ */
 @Category({})
 @BaseWebDriverTest.ClassTimeout(minutes = 3)
 public class TargetedMSSampleManagerIntegrationTest extends TargetedMSPremiumTest

test/src/org/labkey/test/tests/panoramapremium/TargetedMSiRTMetricsTest.java

@@ -18,6 +18,9 @@
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
+/**
+ * Tests iRT metrics calculations and their visualization specifically within the QC dashboard context.
+ */
 @Category({})
 @BaseWebDriverTest.ClassTimeout(minutes = 5)
 public class TargetedMSiRTMetricsTest extends TargetedMSPremiumTest
@@ -223,17 +226,31 @@ private String getChromatogramPlotColor(String peptide)
 
     private void verifyQCPlotColors(String peptide, String color)
     {
+        List<WebElement> treeItems = Locator.css(".qc-tree-precursor").findElements(getDriver());
+        for (WebElement e : treeItems)
+        {
+            String fragment = e.getAttribute("data-fragment");
+            if (fragment != null && fragment.contains(peptide))
+            {
+                checker().verifyEquals("Incorrect color for QC plot for " + peptide, color,
+                        e.getAttribute("data-color"));
+                return;
+            }
+        }
+
+        // Fallback for files without peptide groups (SVG-based legend)
         List<WebElement> legendList = Locator.tagWithClass("g", "legend-item").findElements(getDriver());
         for (WebElement e : legendList)
         {
-            if (e.getAttribute("title").startsWith(peptide + " "))
+            String title = e.getAttribute("title");
+            if (title != null && title.startsWith(peptide + " "))
             {
                 checker().verifyEquals("Incorrect color for QC plot for " + peptide, color,
                         Locator.tag("path").findElement(e).getAttribute("fill"));
                 return;
             }
-
         }
+
         throw new RuntimeException("Did not find the peptide " + peptide);
     }
 }

test/src/org/labkey/test/tests/targetedms/ClustergrammerTest.java

@@ -27,6 +27,9 @@
 
 import java.util.Arrays;
 
+/**
+ * Tests the Clustergrammer heatmap visualization integration for peptide data.
+ */
 @Category({})
 @BaseWebDriverTest.ClassTimeout(minutes = 5)
 public class ClustergrammerTest extends TargetedMSTest

test/src/org/labkey/test/tests/targetedms/GetDataAPITest.java

@@ -27,6 +27,9 @@
 import static org.hamcrest.CoreMatchers.containsString;
 import static org.junit.Assert.assertThat;
 
+/**
+ * Tests the GetData API with query transformations, filtering, and pivot operations on TargetedMS data.
+ */
 @Category({})
 @BaseWebDriverTest.ClassTimeout(minutes = 5)
 public class GetDataAPITest extends TargetedMSTest

test/src/org/labkey/test/tests/targetedms/InstrumentSchedulingTest.java

@@ -48,6 +48,9 @@
 import static org.junit.Assert.assertTrue;
 import static org.junit.Assert.fail;
 
+/**
+ * Tests instrument scheduling workflows including date/time handling and permissions across QC folders.
+ */
 @Category({})
 @FixMethodOrder(MethodSorters.NAME_ASCENDING) // Don't insert additional projects until after testSchedule() has run
 public class InstrumentSchedulingTest extends TargetedMSTest implements PostgresOnlyTest

test/src/org/labkey/test/tests/targetedms/TargetedMSAuditLogTest.java

@@ -10,6 +10,9 @@
 
 import static org.junit.Assert.assertEquals;
 
+/**
+ * Verifies that audit log entries from Skyline documents are correctly imported and displayed as an audit trail.
+ */
 @Category({})
 @BaseWebDriverTest.ClassTimeout(minutes = 5)
 public class TargetedMSAuditLogTest extends TargetedMSTest

test/src/org/labkey/test/tests/targetedms/TargetedMSChromatogramOptimizationTest.java

@@ -20,6 +20,9 @@
 import java.util.LinkedList;
 import java.util.List;
 
+/**
+ * Tests chromatogram optimization workflows and library file generation from imported Skyline documents.
+ */
 @Category({})
 @BaseWebDriverTest.ClassTimeout(minutes = 3)
 public class TargetedMSChromatogramOptimizationTest extends TargetedMSTest

test/src/org/labkey/test/tests/targetedms/TargetedMSDocumentFormatsTest.java

@@ -31,6 +31,9 @@
 import java.util.Collections;
 import java.util.List;
 
+/**
+ * Tests backward compatibility by importing Skyline documents across multiple historical format versions.
+ */
 @Category({})
 public class TargetedMSDocumentFormatsTest extends TargetedMSTest
 {

test/src/org/labkey/test/tests/targetedms/TargetedMSEarlyStagePTMReportTest.java

@@ -12,6 +12,10 @@
 
 import static org.junit.Assert.assertEquals;
 
+/**
+ * Tests the PTM (post-translational modification) peptide report feature, including data pre-pivoting for
+ * early-stage PTM analysis.
+ */
 @Category({})
 public class TargetedMSEarlyStagePTMReportTest extends TargetedMSTest
 {

test/src/org/labkey/test/tests/targetedms/TargetedMSExperimentIrtTest.java

@@ -21,6 +21,9 @@
 
 import static org.junit.Assert.assertEquals;
 
+/**
+ * Tests iRT (indexed Retention Time) scale import in experiment folders, validating the standard peptide set.
+ */
 @Category({})
 @BaseWebDriverTest.ClassTimeout(minutes = 5)
 public class TargetedMSExperimentIrtTest extends TargetedMSIrtTest

test/src/org/labkey/test/tests/targetedms/TargetedMSExperimentTest.java

@@ -56,6 +56,9 @@
 import static org.labkey.test.util.DataRegionTable.DataRegion;
 import static org.labkey.test.util.PermissionsHelper.READER_ROLE;
 
+/**
+ * Broad coverage of experiment folder behavior: file uploads, shared file access, and folder-level permissions.
+ */
 @Category({})
 @BaseWebDriverTest.ClassTimeout(minutes = 8)
 public class TargetedMSExperimentTest extends TargetedMSTest