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Merged
merged 2 commits into from
Jul 9, 2025
Merged

[bot] Merge 25.7 to develop #902

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db51fd0
Fix data region column name references (#901)
labkey-tchad Jul 2, 2025
854c695
Merge 25.7 to develop
labkey-teamcity Jul 9, 2025
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13 changes: 7 additions & 6 deletions ms2/test/src/org/labkey/test/tests/ms2/LibraTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -26,6 +26,7 @@
import org.labkey.test.categories.MS2;
import org.labkey.test.components.CustomizeView;
import org.labkey.test.ms2.MS2TestBase;
import org.labkey.test.params.FieldKey;
import org.labkey.test.util.DataRegionExportHelper;
import org.labkey.test.util.DataRegionTable;
import org.labkey.test.util.TextSearcher;
Expand Down Expand Up @@ -127,9 +128,9 @@ private void spectraCountTest()
// Customize view to pull in other columns
_customizeViewsHelper.openCustomizeViewPanel();
_customizeViewsHelper.addColumn("TrimmedPeptide");
_customizeViewsHelper.addColumn(new String[] {"Protein", "ProtSequence"});
_customizeViewsHelper.addColumn(new String[] {"Protein", "BestName"});
_customizeViewsHelper.addColumn(new String[] {"Protein", "Mass"});
_customizeViewsHelper.addColumn(FieldKey.fromParts("Protein", "ProtSequence"));
_customizeViewsHelper.addColumn(FieldKey.fromParts("Protein", "BestName"));
_customizeViewsHelper.addColumn(FieldKey.fromParts("Protein", "Mass"));
_customizeViewsHelper.saveDefaultView();
assertTextPresent("84731", "MPEETQAQDQPMEEEEVETFAFQAEIAQLM");

Expand All @@ -142,7 +143,7 @@ private void spectraCountTest()
clickAndWait(Locator.linkWithText("Spectra Count Options"));
click(Locator.linkWithText("Create or Edit View"));
findButton("Save");
_customizeViewsHelper.addFilter("Hyper", "Hyper", "Is Greater Than", "250");
_customizeViewsHelper.addFilter("Hyper", "Is Greater Than", "250");
assertRadioButtonSelected(Locator.radioButtonByNameAndValue("spectraConfig", "SpectraCountPeptide"));
_customizeViewsHelper.saveCustomView("HyperFilter");
click(Locator.radioButtonById("SpectraCountPeptideCharge"));
Expand Down Expand Up @@ -219,7 +220,7 @@ private void addNormalizationCount(CustomizeView customizeView)
{
for (int i = 1; i <= normalizationCount; i++)
{
customizeView.addColumn("iTRAQQuantitation/Normalized" + i, "Normalized " + i);
customizeView.addColumn("iTRAQQuantitation/Normalized" + i);
}
}

Expand All @@ -231,7 +232,7 @@ private void proteinProphetTest()

for (int i = 1; i <= normalizationCount; i++)
{
customizeView.addColumn("ProteinProphetData/ProteinGroupId/iTRAQQuantitation/Ratio" + i, "Ratio " + i);
customizeView.addColumn("ProteinProphetData/ProteinGroupId/iTRAQQuantitation/Ratio" + i);
}
addNormalizationCount(customizeView);
customizeView.saveCustomView(proteinProphetView);
Expand Down
63 changes: 33 additions & 30 deletions ms2/test/src/org/labkey/test/tests/ms2/MS2Test.java
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Original file line number Diff line number Diff line change
Expand Up @@ -24,10 +24,10 @@
import org.labkey.test.WebTestHelper;
import org.labkey.test.categories.Daily;
import org.labkey.test.categories.MS2;
import org.labkey.test.params.FieldKey;
import org.labkey.test.util.AbstractDataRegionExportOrSignHelper.ColumnHeaderType;
import org.labkey.test.util.DataRegionExportHelper;
import org.labkey.test.util.DataRegionTable;
import org.labkey.test.util.EscapeUtil;
import org.labkey.test.util.LogMethod;
import org.labkey.test.util.TextSearcher;
import org.openqa.selenium.WebElement;
Expand Down Expand Up @@ -397,21 +397,22 @@ private void verifyFirstRun()
log("Check that saved view is working");
assertTextNotPresent("K.KTEENYTLVFIVDVK.A");

DataRegionTable innerTable = DataRegionTable.DataRegion(getDriver()).withName(REGION_NAME_PEPTIDES).find(peptidesTable);
log("Test adding a sort and a filter");
peptidesTable.setFilter("Hyper", "Is Greater Than", "10.6");
innerTable.setFilter("Hyper", "Is Greater Than", "10.6");
assertTextNotPresent("K.RFSGTVKLK.Y");
peptidesTable.setSort("Next", SortDirection.ASC);
innerTable.setSort("Next", SortDirection.ASC);
// Explicitly clear out the sorts, since we want to be just dealing with the ones set in Customize View
peptidesTable.clearSort("Next");
peptidesTable.clearSort("Scan");
innerTable.clearSort("Next");
innerTable.clearSort("Scan");

log("Test customize view");
peptidesTable.clearAllFilters();
_customizeViewsHelper.openCustomizeViewPanel();
_customizeViewsHelper.addSort("Charge", "Z", SortDirection.DESC);
_customizeViewsHelper.addSort("Mass", "CalcMH+", SortDirection.DESC);
_customizeViewsHelper.addFilter("DeltaMass", "dMass", "Is Less Than", "0");
_customizeViewsHelper.addColumn("NextAA", "Next AA");
_customizeViewsHelper.addSort("Charge", SortDirection.DESC);
_customizeViewsHelper.addSort("Mass", SortDirection.DESC);
_customizeViewsHelper.addFilter("DeltaMass", "Is Less Than", "0");
_customizeViewsHelper.addColumn("NextAA");
_customizeViewsHelper.removeColumn("Expect");
_customizeViewsHelper.removeColumn("ProteinHits");
_customizeViewsHelper.saveCustomView(VIEW4);
Expand Down Expand Up @@ -515,8 +516,8 @@ private void verifyFirstRun()
_customizeViewsHelper.openCustomizeViewPanel();
_customizeViewsHelper.clearFilters();
_customizeViewsHelper.clearSorts();
_customizeViewsHelper.addSort("DeltaMass", "dMass", SortDirection.ASC);
_customizeViewsHelper.addFilter("Mass", "CalcMH+", "Is Greater Than", "1000");
_customizeViewsHelper.addSort("DeltaMass", SortDirection.ASC);
_customizeViewsHelper.addFilter("Mass", "Is Greater Than", "1000");
_customizeViewsHelper.addColumn("Fraction");
_customizeViewsHelper.removeColumn("IonPercent");
_customizeViewsHelper.saveDefaultView();
Expand Down Expand Up @@ -551,14 +552,14 @@ private void verifyFirstRun()

log("Test Protein Prophet view in Query - Peptides grouping");
_customizeViewsHelper.openCustomizeViewPanel();
_customizeViewsHelper.addColumn("ProteinProphetData/ProteinGroupId/Group", "Group");
_customizeViewsHelper.addColumn("ProteinProphetData/ProteinGroupId/TotalNumberPeptides", "Peptides");
_customizeViewsHelper.addColumn("ProteinProphetData/ProteinGroupId/GroupProbability", "Prob");
_customizeViewsHelper.addColumn("ProteinProphetData/ProteinGroupId/BestName", "Best Name");
_customizeViewsHelper.addColumn("ProteinProphetData/ProteinGroupId/Group");
_customizeViewsHelper.addColumn("ProteinProphetData/ProteinGroupId/TotalNumberPeptides");
_customizeViewsHelper.addColumn("ProteinProphetData/ProteinGroupId/GroupProbability");
_customizeViewsHelper.addColumn("ProteinProphetData/ProteinGroupId/BestName");
_customizeViewsHelper.removeColumn("Mass");
_customizeViewsHelper.addFilter("DeltaMass", "dMass", "Is Greater Than", "0");
_customizeViewsHelper.addFilter("ProteinProphetData/ProteinGroupId/GroupProbability", "Prob", "Is Greater Than", "0.7");
_customizeViewsHelper.addSort("ProteinProphetData/ProteinGroupId/GroupProbability", "Prob", SortDirection.ASC);
_customizeViewsHelper.addFilter("DeltaMass", "Is Greater Than", "0");
_customizeViewsHelper.addFilter("ProteinProphetData/ProteinGroupId/GroupProbability", "Is Greater Than", "0.7");
_customizeViewsHelper.addSort("ProteinProphetData/ProteinGroupId/GroupProbability", SortDirection.ASC);
_customizeViewsHelper.saveCustomView(VIEW4);

log("Test that Protein Prophet view is displayed and that it sorts and filters correctly");
Expand Down Expand Up @@ -621,9 +622,9 @@ private void verifyFirstRun()
log("Test customize view");
_customizeViewsHelper.openCustomizeViewPanel();
_customizeViewsHelper.removeColumn("UniquePeptidesCount");
_customizeViewsHelper.addColumn("Proteins/Protein/ProtSequence", "Protein Sequence");
_customizeViewsHelper.addFilter("GroupProbability", "Prob", "Is Greater Than", "0.7");
_customizeViewsHelper.addSort("ErrorRate", "Error", SortDirection.DESC);
_customizeViewsHelper.addColumn("Proteins/Protein/ProtSequence");
_customizeViewsHelper.addFilter("GroupProbability", "Is Greater Than", "0.7");
_customizeViewsHelper.addSort("ErrorRate", SortDirection.DESC);
_customizeViewsHelper.saveCustomView(VIEW4);

log("Test that sorting, filtering, and columns are correct");
Expand Down Expand Up @@ -833,13 +834,14 @@ private void validateRunGroups()
setFormElement(Locator.name("name"), RUN_GROUP1_NAME2);
clickButton("Submit");

FieldKey runGroupFK = FieldKey.fromParts("RunGroupToggle");
log("Test customizing view to include the run groups");
navigateToFolder(FOLDER_NAME);
clickAndWait(Locator.linkWithText("MS2 Runs"));
_customizeViewsHelper.openCustomizeViewPanel();
_customizeViewsHelper.addColumn(new String[] { "RunGroupToggle", EscapeUtil.fieldKeyEncodePart(RUN_GROUP1_NAME2) }, RUN_GROUP1_NAME2);
_customizeViewsHelper.addColumn(new String[]{"RunGroupToggle", RUN_GROUP2_NAME}, "Run Groups " + RUN_GROUP2_NAME);
_customizeViewsHelper.addColumn(new String[]{"RunGroupToggle", "Default Experiment"}, "Run Groups Default Experiment");
_customizeViewsHelper.addColumn(runGroupFK.child(RUN_GROUP1_NAME2));
_customizeViewsHelper.addColumn(runGroupFK.child(RUN_GROUP2_NAME));
_customizeViewsHelper.addColumn(runGroupFK.child("Default Experiment"));
_customizeViewsHelper.applyCustomView();

assertTextPresent(new TextSearcher(this).setSearchTransformer(TextSearcher.TextTransformers.FIELD_LABEL),
Expand Down Expand Up @@ -876,8 +878,8 @@ private void validateRunGroups()

log("Test Customize View");
_customizeViewsHelper.openCustomizeViewPanel();
_customizeViewsHelper.addColumn("SeqId/Mass", "Protein Mass");
_customizeViewsHelper.addFilter("SeqId/Mass", "Protein Mass", "Is Less Than", "30000");
_customizeViewsHelper.addColumn("SeqId/Mass");
_customizeViewsHelper.addFilter("SeqId/Mass", "Is Less Than", "30000");
_customizeViewsHelper.saveCustomView(VIEW5);

DataRegionTable peptidesTable = new DataRegionTable("query", this);
Expand Down Expand Up @@ -1110,7 +1112,7 @@ private void validateCompare()
_customizeViewsHelper.openCustomizeViewPanel();
_customizeViewsHelper.addColumn("CTAGG_AVG_XCorr");
_customizeViewsHelper.removeColumn("InstanceCount");
_customizeViewsHelper.addFilter("CTAGG_AVG_XCorr", "Avg XCorr", "Is Greater Than", "10");
_customizeViewsHelper.addFilter("CTAGG_AVG_XCorr", "Is Greater Than", "10");
_customizeViewsHelper.saveCustomView();

log("Check filtering and columns were added correctly");
Expand Down Expand Up @@ -1246,17 +1248,18 @@ private void validateContainerFilter()
DataRegionTable dataTable = viewQueryData("ms2", "XTandemPeptides");
dataTable.setContainerFilter(DataRegionTable.ContainerFilterType.CURRENT_AND_SUBFOLDERS);

FieldKey runGroupsFk = FieldKey.fromParts("Fraction", "Run", "ExperimentRunLSID", "RunGroups");
_customizeViewsHelper.openCustomizeViewPanel();
_customizeViewsHelper.addColumn(new String[]{"Fraction", "Run", "ExperimentRunLSID", "RunGroups"});
_customizeViewsHelper.addColumn(runGroupsFk);
_customizeViewsHelper.applyCustomView();
assertNotEquals("All rows should have a value for the run group", 0, dataTable.getDataRowCount());

// validate a single run group with the expected label
Set<String> runGroups = new HashSet<>(dataTable.getColumnDataAsText("RunGroups"));
Set<String> runGroups = new HashSet<>(dataTable.getColumnDataAsText(runGroupsFk));
assertEquals("Incorrect number of run groups", 1, runGroups.size());
assertEquals("Invalid run group label", RUN_GROUP3_NAME, runGroups.iterator().next());

dataTable.setFilter("Fraction/Run/ExperimentRunLSID/RunGroups", "Is Blank");
dataTable.setFilter(runGroupsFk, "Is Blank");
assertEquals("All rows should have a value for the run group", 0, dataTable.getDataRowCount());
}
}
9 changes: 5 additions & 4 deletions ms2/test/src/org/labkey/test/tests/ms2/SequestImportTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -24,6 +24,7 @@
import org.labkey.test.categories.Daily;
import org.labkey.test.categories.MS2;
import org.labkey.test.components.CustomizeView;
import org.labkey.test.params.FieldKey;
import org.labkey.test.util.DataRegionTable;
import org.labkey.test.util.FileBrowserHelper;
import org.labkey.test.util.LogMethod;
Expand All @@ -38,8 +39,8 @@ public class SequestImportTest extends BaseWebDriverTest
{
private static final String PROJECT_NAME = "SequestImport" + TRICKY_CHARACTERS_FOR_PROJECT_NAMES;

private static final String[] TOTAL_PEPTIDES_FIELD_KEY = {"PeptideCounts", "TotalPeptides"};
private static final String[] UNIQUE_PEPTIDES_FIELD_KEY = {"PeptideCounts", "DistinctPeptides"};
private static final FieldKey TOTAL_PEPTIDES_FIELD_KEY = FieldKey.fromParts("PeptideCounts", "TotalPeptides");
private static final FieldKey UNIQUE_PEPTIDES_FIELD_KEY = FieldKey.fromParts("PeptideCounts", "DistinctPeptides");

@Override
protected String getProjectName()
Expand Down Expand Up @@ -69,8 +70,8 @@ private void verifyRunGrid()
viewsHelper.addColumn(UNIQUE_PEPTIDES_FIELD_KEY);

// Add a filter so that we can check the values were calculated and shown correctly
viewsHelper.addFilter(TOTAL_PEPTIDES_FIELD_KEY, "Total Peptides", "Equals", "2");
viewsHelper.addFilter(UNIQUE_PEPTIDES_FIELD_KEY, "Distinct Peptides", "Equals", "1");
viewsHelper.addFilter(TOTAL_PEPTIDES_FIELD_KEY, "Equals", "2");
viewsHelper.addFilter(UNIQUE_PEPTIDES_FIELD_KEY, "Equals", "1");
viewsHelper.saveDefaultView();

// Make sure that our run is still showing
Expand Down