-
<%= h(StringUtilsLabKey.pluralize(run.getPeptideGroupCount(), peptideGroupLabel))%>,
- <% if (run.getPeptideCount() > 0) { %>
<%= h(StringUtilsLabKey.pluralize(run.getPeptideCount(), "peptide"))%>,<% } %>
- <% if (run.getSmallMoleculeCount() > 0) { %>
"><%= h(StringUtilsLabKey.pluralize(run.getSmallMoleculeCount(), "small molecule"))%>,<% } %>
+ <% if (run.getPeptideGroupCount() > 0) { %>
<%= h(StringUtilsLabKey.pluralize(run.getPeptideGroupCount(), "protein group"))%><%
+ if (run.getProteinCount() > 0) { %> (with
<%= h(StringUtilsLabKey.pluralize(run.getProteinCount(), "protein"))%>)<% } %>,
+ <% } %>
+ <% if (run.getMoleculeGroupCount() > 0) { %>
<%= h(StringUtilsLabKey.pluralize(run.getMoleculeGroupCount(), "molecule list"))%>,<% } %>
+ <% if (run.getPeptideCount() > 0) { %>
<%= h(StringUtilsLabKey.pluralize(run.getPeptideCount(), "peptide"))%>,<% } %>
+ <% if (run.getSmallMoleculeCount() > 0) { %>
<%= h(StringUtilsLabKey.pluralize(run.getSmallMoleculeCount(), "small molecule"))%>,<% } %>
<%= h(StringUtilsLabKey.pluralize(run.getPrecursorCount(), "precursor"))%>,
<%= h(StringUtilsLabKey.pluralize(run.getTransitionCount(), "transition"))%>
-
diff --git a/test/src/org/labkey/test/pages/panoramapremium/ConfigureMetricsUIPage.java b/test/src/org/labkey/test/pages/panoramapremium/ConfigureMetricsUIPage.java
index b87419916..ae9a4a7fb 100644
--- a/test/src/org/labkey/test/pages/panoramapremium/ConfigureMetricsUIPage.java
+++ b/test/src/org/labkey/test/pages/panoramapremium/ConfigureMetricsUIPage.java
@@ -7,7 +7,6 @@
import org.labkey.test.components.targetedms.QCPlotsWebPart;
import org.labkey.test.pages.PortalBodyPanel;
import org.labkey.test.util.Ext4Helper;
-import org.openqa.selenium.NoSuchElementException;
import org.openqa.selenium.WebDriver;
import java.util.Map;
@@ -16,6 +15,7 @@ public class ConfigureMetricsUIPage extends PortalBodyPanel
{
public static final String ADD_NEW_CUSTOM_METRIC = "Add New Custom Metric";
+ public static final String ADD_NEW_ANNOTATION_METRIC = "Add Annotation-Backed Metric";
public ConfigureMetricsUIPage(WebDriver driver)
{
@@ -121,9 +121,18 @@ public String clickSaveExpectingError()
public void addNewCustomMetric(Map
metricProperties, boolean duplicateNameErrorExpected)
{
click(Locator.tagWithText("button", ADD_NEW_CUSTOM_METRIC));
- waitForElement(Ext4Helper.Locators.window("Add New Metric"));
- Window metricWindow = new Window.WindowFinder(getDriver()).withTitle("Add New Metric").waitFor();
- editCustomMetricValues(metricWindow, metricProperties, duplicateNameErrorExpected);
+ waitForCustomMetricDialog();
+ fillCustomMetricForm(metricProperties);
+ if (duplicateNameErrorExpected)
+ {
+ click(Locator.id("lk-custom-metric-save"));
+ assertTextPresent("A metric with the name \"" + metricProperties.get(CustomMetricProperties.metricName) + "\" already exists. Please choose a different name.");
+ click(Locator.id("lk-custom-metric-cancel"));
+ }
+ else
+ {
+ clickAndWait(Locator.id("lk-custom-metric-save"));
+ }
}
public void addNewTraceMetric(Map traceProperties, boolean duplicateNameErrorExpected)
@@ -134,56 +143,80 @@ public void addNewTraceMetric(Map traceProperties
editTraceMetricValues(metricWindow, traceProperties, duplicateNameErrorExpected);
}
+ public void addNewAnnotationMetric(Map metricProperties, boolean duplicateNameErrorExpected)
+ {
+ click(Locator.tagWithText("button", ADD_NEW_ANNOTATION_METRIC));
+ waitForAnnotationDialog();
+ fillAnnotationForm(metricProperties);
+ if (duplicateNameErrorExpected)
+ {
+ click(Locator.id("lk-annotation-metric-save"));
+ String metricName = metricProperties.get(AnnotationMetricProperties.metricName);
+ assertTextPresent("A metric with the name \"" + metricName + "\" already exists. Please choose a different name.");
+ click(Locator.id("lk-annotation-metric-cancel"));
+ }
+ else
+ {
+ clickAndWait(Locator.id("lk-annotation-metric-save"));
+ }
+ }
+
+ public void editAnnotationMetric(String metric, Map metricProperties)
+ {
+ waitAndClick(Locator.linkWithText(metric));
+ waitForAnnotationDialog();
+ fillAnnotationForm(metricProperties);
+ clickAndWait(Locator.id("lk-annotation-metric-save"));
+ }
+
+ public void deleteAnnotationMetric(String metric)
+ {
+ waitAndClick(Locator.linkWithText(metric));
+ waitForAnnotationDialog();
+ click(Locator.id("lk-annotation-metric-delete"));
+ acceptAlert();
+ waitForPage();
+ waitForElementToDisappear(Locator.linkWithText(metric));
+ }
+
public void editMetric(String metric, Map metricProperties)
{
- Window metricWindow = openForEdit(metric);
- editCustomMetricValues(metricWindow, metricProperties, false);
+ openForEdit(metric);
+ fillCustomMetricForm(metricProperties);
+ clickAndWait(Locator.id("lk-custom-metric-save"));
}
public void deleteMetric(String metric)
{
openForEdit(metric);
- clickButton("Delete", 0);
- clickButton("Yes");
- waitForPage();
+ doAndWaitForPageToLoad(() -> {
+ click(Locator.id("lk-custom-metric-delete"));
+ acceptAlert();
+ });
}
- private Window openForEdit(String metric)
+ private void openForEdit(String metric)
{
waitAndClick(Locator.linkWithText(metric));
- waitForElement(Ext4Helper.Locators.window("Edit Metric"));
- return new Window.WindowFinder(getDriver()).withTitle("Edit Metric").waitFor();
+ waitForCustomMetricDialog();
}
- private void editCustomMetricValues(Window metricWindow, Map metricProperties, boolean duplicateNameErrorExpected)
+ private void waitForCustomMetricDialog()
{
- metricProperties.forEach((prop, val) -> {
- if (!prop.isSelect)
- {
- setFormElement(Locator.name(prop.name()), val);
- }
- else
- {
- String label = prop.formLabel;
- //adding waits does not help here, however it passes in catch block
- try
- {
- _ext4Helper.selectComboBoxItem(label, val);
- }
- catch (NoSuchElementException e)
- {
- _ext4Helper.selectComboBoxItem(label, val);
- }
- }
- });
- if (duplicateNameErrorExpected)
- {
- duplicateNameErrorExpected(metricProperties.get(CustomMetricProperties.metricName));
- }
- else
- {
- clickAndWait(Ext4Helper.Locators.ext4Button("Save").findElement(metricWindow));
- }
+ waitForElement(Locator.id("lk-custom-metric-dialog"));
+ waitForElement(Locator.tagWithText("option", "-- Select query --"));
+ }
+
+ private void fillCustomMetricForm(Map props)
+ {
+ if (props.containsKey(CustomMetricProperties.metricName))
+ setFormElement(Locator.id("lk-custom-metric-name"), props.get(CustomMetricProperties.metricName));
+ if (props.containsKey(CustomMetricProperties.yAxisLabel))
+ setFormElement(Locator.id("lk-custom-metric-ylabel"), props.get(CustomMetricProperties.yAxisLabel));
+ if (props.containsKey(CustomMetricProperties.metricType))
+ click(Locator.css("input[name='customMetricType'][value='" + props.get(CustomMetricProperties.metricType).toLowerCase() + "']"));
+ if (props.containsKey(CustomMetricProperties.queryName))
+ selectOptionByText(Locator.id("lk-custom-metric-query"), props.get(CustomMetricProperties.queryName));
}
private void editTraceMetricValues(Window metricWindow, Map metricProperties, boolean duplicateNameErrorExpected)
@@ -215,11 +248,33 @@ else if (prop.formLabel != null)
}
}
+ private void waitForAnnotationDialog()
+ {
+ waitForElement(Locator.id("lk-annotation-metric-dialog"));
+ waitForElement(Locator.tagWithText("option", "-- Select annotation --"));
+ }
+
+ private void fillAnnotationForm(Map props)
+ {
+ if (props.containsKey(AnnotationMetricProperties.metricName))
+ setFormElement(Locator.id("lk-annotation-metric-name"), props.get(AnnotationMetricProperties.metricName));
+ if (props.containsKey(AnnotationMetricProperties.yAxisLabel))
+ setFormElement(Locator.id("lk-annotation-metric-ylabel"), props.get(AnnotationMetricProperties.yAxisLabel));
+ if (props.containsKey(AnnotationMetricProperties.annotationType))
+ click(Locator.css("input[name='annotationType'][value='" + props.get(AnnotationMetricProperties.annotationType) + "']"));
+ if (props.containsKey(AnnotationMetricProperties.annotationName))
+ {
+ String annotationName = props.get(AnnotationMetricProperties.annotationName);
+ waitForElement(Locator.tagWithText("option", annotationName));
+ selectOptionByText(Locator.id("lk-annotation-name-select"), annotationName);
+ }
+ }
+
private void duplicateNameErrorExpected(String metricName)
{
- click(Ext4Helper.Locators.ext4Button("Save"));
+ click(Locator.id("lk-custom-metric-save"));
assertTextPresent("A metric with the name \"" + metricName + "\" already exists. Please choose a different name.");
- click(Ext4Helper.Locators.ext4Button("Cancel"));
+ click(Locator.id("lk-custom-metric-cancel"));
}
public void clearMetricCache()
@@ -251,6 +306,14 @@ public enum CustomMetricProperties
}
}
+ public enum AnnotationMetricProperties
+ {
+ metricName,
+ yAxisLabel,
+ annotationType, // "replicate" or "precursor"
+ annotationName
+ }
+
public enum TraceMetricProperties
{
metricName(null, false),
diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSExperimentTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSExperimentTest.java
index 2f70382b3..6430a5336 100644
--- a/test/src/org/labkey/test/tests/targetedms/TargetedMSExperimentTest.java
+++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSExperimentTest.java
@@ -90,6 +90,7 @@ public void testSteps() throws IOException, CommandException
verifyImportedSmallMoleculeData();
verifyAttributeGroupIdCalcs();
testRawFileLinks(SKY_FILE_SMALLMOL_PEP);
+ verifyRunDetailLinks();
// SKYD version 14
importData(SKY_FILE_SKYD_14, ++jobCount);
@@ -165,7 +166,7 @@ protected void verifyImportedPeptideData()
{
clickAndWait(Locator.linkContainingText("Panorama Dashboard"));
clickAndWait(Locator.linkContainingText(SKY_FILE));
- verifyRunSummaryCountsPep(24,44,0, 88,296, 1, 0, 0);
+ verifyRunSummaryCountsPep(24, 24, 44, 0, 88, 296, 1, 0, 0);
verifyDocumentDetails(false);
verifyPeptide();
}
@@ -175,7 +176,7 @@ protected void verifyImportedSmallMoleculeData()
{
clickAndWait(Locator.linkContainingText("Panorama Dashboard"));
clickAndWait(Locator.linkContainingText(SKY_FILE_SMALLMOL_PEP));
- verifyRunSummaryCountsSmallMol(27, 44, 98, 186, 394, 5, 0, 0); // Number of protein (groups), peptides, precursors, transitions, small molecules
+ verifyRunSummaryCountsMixed(24, 3, 24, 44, 98, 186, 394, 5, 0, 0);
verifyDocumentDetails(true);
verifyMolecule();
}
@@ -895,4 +896,54 @@ private void verifyNoGuestAccessMessage(boolean selfSignupEnabled)
assertFalse(fullBodyText.contains("Don't have an account? Register"));
}
}
+
+ @LogMethod
+ protected void verifyRunDetailLinks()
+ {
+ // From the runs listing (Panorama Dashboard), clicking a run's name navigates to the default
+ // run view. A mixed proteomics + small molecule document shows both precursor grids there.
+ // precursors_view is nested by protein group (24 total groups, 10 shown per page due to maxRows).
+ // getDataRowCount() returns outer rows + even-indexed expanded rows: 5+5+5=15 for 10 groups.
+ // small_mol_precursors_view has 3 molecule groups (all fit on one page): 2+1+2=5.
+ goToDashboard();
+ clickAndWait(Locator.linkContainingText(SKY_FILE_SMALLMOL_PEP));
+ DataRegionTable precursorsView = DataRegion(getDriver()).withName("precursors_view").find();
+ assertEquals(15, precursorsView.getDataRowCount());
+ DataRegionTable smallMolPrecursorsView = DataRegion(getDriver()).withName("small_mol_precursors_view").find();
+ assertEquals(5, smallMolPrecursorsView.getDataRowCount());
+
+ // Test each header link from runSummaryView.jsp while on the default run view.
+ // Each link must reach its own dedicated list page, not the combined precursor list.
+
+ // "24 protein groups" → protein group list: one row per peptide-bearing group
+ clickAndWait(Locator.linkContainingText("24 protein groups"));
+ DataRegionTable peptideGroupView = DataRegion(getDriver()).withName("PeptideGroup").find();
+ assertEquals(24, peptideGroupView.getDataRowCount());
+
+ // "3 molecule lists" → molecule group list: one row per molecule-bearing group
+ clickAndWait(Locator.linkContainingText("3 molecule lists"));
+ DataRegionTable moleculeGroupView = DataRegion(getDriver()).withName("MoleculeGroup").find();
+ assertEquals(3, moleculeGroupView.getDataRowCount());
+
+ // "44 peptides" → peptide list page: one row per peptide
+ clickAndWait(Locator.linkContainingText("44 peptides"));
+ DataRegionTable peptideView = DataRegion(getDriver()).withName("Peptide").find();
+ assertEquals(44, peptideView.getDataRowCount());
+
+ // "98 small molecules" → small molecule list page: one row per molecule
+ clickAndWait(Locator.linkContainingText("98 small molecules"));
+ DataRegionTable moleculeView = DataRegion(getDriver()).withName("Molecule").find();
+ assertEquals(98, moleculeView.getDataRowCount());
+
+ // Verify the runSummaryView.jsp header links also work when on a non-default run detail page.
+ // The header is embedded on every run detail view, not just the precursor list.
+ // From the small molecule list page, click "24 protein groups".
+ clickAndWait(Locator.linkContainingText("24 protein groups"));
+ peptideGroupView = DataRegion(getDriver()).withName("PeptideGroup").find();
+ assertEquals(24, peptideGroupView.getDataRowCount());
+ // From the protein group list page, click "44 peptides".
+ clickAndWait(Locator.linkContainingText("44 peptides"));
+ peptideView = DataRegion(getDriver()).withName("Peptide").find();
+ assertEquals(44, peptideView.getDataRowCount());
+ }
}
diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSLibraryTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSLibraryTest.java
index c10a8793a..9f91dcdda 100644
--- a/test/src/org/labkey/test/tests/targetedms/TargetedMSLibraryTest.java
+++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSLibraryTest.java
@@ -29,6 +29,7 @@
import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
+import java.util.stream.IntStream;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
@@ -111,7 +112,7 @@ protected void verifyRevision1()
// Verify proteins in the library
// Proteins in SKY_FILE1: "CTCF", "TAF11", "MAX", "QPrEST_CystC_HPRR5000001", "HPRR1440042", "DifferentProteinSameLabel", "iRT-C18 Standard Peptides"
List proteins = Arrays.asList("CTCF", "TAF11", "MAX", "QPrEST_CystC_HPRR5000001", "HPRR1440042", "DifferentProteinSameLabel", "iRT-C18 Standard Peptides");
- List files = new ArrayList();
+ List files = new ArrayList<>();
for (int i = 0; i < proteins.size(); i++)
{
files.add(SKY_FILE1); // All proteins are from the same file in version 1.
@@ -132,7 +133,9 @@ private void verifyLibraryProteins(List proteins, List files, in
int i = 0;
for(String protein: proteins)
{
- int idx = proteinsTable.getRowIndex("Label", protein);
+ int idx = IntStream.range(0, proteinsTable.getDataRowCount())
+ .filter(row -> protein.equals(proteinsTable.getDataAsText(row, "Label")))
+ .findFirst().orElse(-1);
assertTrue("Expected protein " + protein + " not found in table", idx != -1);
ListfileName = proteinsTable.getRowDataAsText(idx, "RunId/File");
assertEquals(1, fileName.size());
@@ -275,8 +278,8 @@ private void verifyAndResolveConflicts()
var proteinName = "MAX";
var oldProteinCb = getCheckBox(proteinName, true).waitForElement(shortWait());
var newProteinCb = getCheckBox(proteinName, false).waitForElement(shortWait());
- assertTrue(isChecked(newProteinCb)); // checkbox for the protein in the new document should be checked
- assertFalse(isChecked(oldProteinCb)); // checkbox for the protein in the old document should be unchecked
+ assertTrue(newProteinCb.isSelected()); // checkbox for the protein in the new document should be checked
+ assertFalse(oldProteinCb.isSelected()); // checkbox for the protein in the old document should be unchecked
// check, uncheck and check again (See Issue 44424)
changeChecked(oldProteinCb, newProteinCb , true, proteinName);
changeChecked(oldProteinCb, newProteinCb , false, proteinName);
@@ -290,13 +293,13 @@ private void changeChecked(WebElement oldProteinCb, WebElement newProteinCb, boo
setCheckbox(oldProteinCb, selectOld);
if (selectOld)
{
- assertFalse("Expected " + proteinName + " from the new document to be unchecked", isChecked(newProteinCb)); // new protein unchecked
- assertTrue("Expected " + proteinName + " from the old document to be checked", isChecked(oldProteinCb)); // old protein checked
+ assertFalse("Expected " + proteinName + " from the new document to be unchecked", newProteinCb.isSelected()); // new protein unchecked
+ assertTrue("Expected " + proteinName + " from the old document to be checked", oldProteinCb.isSelected()); // old protein checked
}
else
{
- assertTrue("Expected " + proteinName + " from the new document to be checked", isChecked(newProteinCb)); // new protein checked
- assertFalse("Expected " + proteinName + " from the old document to be unchecked", isChecked(oldProteinCb)); // old protein unchecked
+ assertTrue("Expected " + proteinName + " from the new document to be checked", newProteinCb.isSelected()); // new protein checked
+ assertFalse("Expected " + proteinName + " from the old document to be unchecked", oldProteinCb.isSelected()); // old protein unchecked
}
}
diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSListTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSListTest.java
index 8ef5ee315..61c180dcd 100644
--- a/test/src/org/labkey/test/tests/targetedms/TargetedMSListTest.java
+++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSListTest.java
@@ -53,13 +53,13 @@ public void testSteps() throws IOException, CommandException
clickAndWait(Locator.linkContainingText("Panorama Dashboard"));
clickAndWait(Locator.linkContainingText(LIST_SKY_FILE_1));
- verifyRunSummaryCountsPep(2,4,0, 5,53, 1, 0, 6);
+ verifyRunSummaryCountsPep(2, 2, 4, 0, 5, 53, 1, 0, 6);
clickAndWait(Locator.linkContainingText("6 lists"));
assertTextPresent("DocumentProperties", "Lorem Ipsum", "Protein Descriptions");
clickAndWait(Locator.linkContainingText("Protein Descriptions"));
// Check that the document header remains
- verifyRunSummaryCountsPep(2,4,0, 5,53, 1, 0, 6);
+ verifyRunSummaryCountsPep(2, 2, 4, 0, 5, 53, 1, 0, 6);
assertTextPresent("ALBU_BOVIN", "main protein of plasma");
List queryNames = validateSampleInfo(1, Set.of("Mickey"), 5, 12);
diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSMAMTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSMAMTest.java
index d02585d6d..d390ddee1 100644
--- a/test/src/org/labkey/test/tests/targetedms/TargetedMSMAMTest.java
+++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSMAMTest.java
@@ -49,7 +49,7 @@ public void testSteps()
clickAndWait(Locator.linkContainingText("Panorama Dashboard"));
clickAndWait(Locator.linkContainingText(SKY_FILE));
- verifyRunSummaryCountsPep(125,158,0, 160,628, 1, 0, 0);
+ verifyRunSummaryCountsPep(125, 124, 158, 0, 160, 628, 1, 0, 0);
clickAndWait(Locator.linkContainingText("PTM Report"));
@@ -82,7 +82,7 @@ public void testCrossLinkedPeptideMap()
clickAndWait(Locator.linkContainingText("Panorama Dashboard"));
clickAndWait(Locator.linkContainingText(CROSS_LINKED_SKY_FILE));
- verifyRunSummaryCountsPep(2,2,0, 2,2, 1, 0, 0);
+ verifyRunSummaryCountsPep(2, 2, 2, 0, 2, 2, 1, 0, 0);
clickAndWait(Locator.linkContainingText("Peptide Map"));
assertTextPresentInThisOrder("121-124", "342-345", "142-145");
diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSProteinGroupingTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSProteinGroupingTest.java
index dd285d028..f61286f6c 100644
--- a/test/src/org/labkey/test/tests/targetedms/TargetedMSProteinGroupingTest.java
+++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSProteinGroupingTest.java
@@ -46,6 +46,7 @@ public void testProteinGrouping()
goToProjectHome();
clickAndWait(Locator.linkWithText(SKY_FILE));
+ verifyRunSummaryCountsPep(31, 47, 33, 0, 33, 198, 4, 0, 0);
clickAndWait(Locator.linkWithText(group));
log("Verifying protein matches for peptide");
diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSQCConfigureMetricTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSQCConfigureMetricTest.java
index e34b17b0f..6095cfd79 100644
--- a/test/src/org/labkey/test/tests/targetedms/TargetedMSQCConfigureMetricTest.java
+++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSQCConfigureMetricTest.java
@@ -23,7 +23,7 @@
* Tests the QC metric configuration UI and verifies settings propagate consistently across folder hierarchies.
*/
@Category({})
-@BaseWebDriverTest.ClassTimeout(minutes = 5)
+@BaseWebDriverTest.ClassTimeout(minutes = 15)
public class TargetedMSQCConfigureMetricTest extends TargetedMSPremiumTest
{
private final static String SUBFOLDER_1 = "QC Subfolder 1";
@@ -206,6 +206,54 @@ public void testPlotOnlyOption()
verifyOutlierCount(replicate, metric, "N/A");
}
+ @Test
+ public void testAnnotationBackedMetric()
+ {
+ String subfolderName = "AnnotationMetricsFolder";
+ String metricName = "Annotation Metric R Squared";
+ String yAxisLabel = "R Squared";
+ String updatedYAxisLabel = "Updated R Squared";
+
+ log("Create subfolder and import data with numeric precursor_result annotations");
+ setupSubfolder(getProjectName(), subfolderName, FolderType.QC);
+ importData(ISOTOPOLOGUE_FILE_ANNOTATED);
+ navigateToFolder(getProjectName(), subfolderName);
+
+ log("Add annotation-backed metric backed by the RSquared precursor annotation");
+ ConfigureMetricsUIPage configureQCMetrics = goToDashboard().getQcSummaryWebPart().clickConfigureQCMetrics();
+ configureQCMetrics.addNewAnnotationMetric(Map.of(
+ ConfigureMetricsUIPage.AnnotationMetricProperties.metricName, metricName,
+ ConfigureMetricsUIPage.AnnotationMetricProperties.yAxisLabel, yAxisLabel,
+ ConfigureMetricsUIPage.AnnotationMetricProperties.annotationType, "precursor",
+ ConfigureMetricsUIPage.AnnotationMetricProperties.annotationName, "RSquared"), false);
+
+ log("Verify metric appears in configure QC metrics table");
+ waitForElement(Locator.linkWithText(metricName));
+
+ goToDashboard();
+ log("Verify metric appears in QC plots dropdown");
+ QCPlotsWebPart qcPlotsWebPart = new PanoramaDashboard(this).getQcPlotsWebPart();
+ Assert.assertTrue("Annotation-backed metric should appear in QC plots dropdown",
+ verifyMetricIsPresent(qcPlotsWebPart, metricName));
+
+ log("Test that a duplicate metric name is rejected");
+ configureQCMetrics = goToDashboard().getQcSummaryWebPart().clickConfigureQCMetrics();
+ configureQCMetrics.addNewAnnotationMetric(Map.of(
+ ConfigureMetricsUIPage.AnnotationMetricProperties.metricName, metricName,
+ ConfigureMetricsUIPage.AnnotationMetricProperties.yAxisLabel, "Duplicate Label",
+ ConfigureMetricsUIPage.AnnotationMetricProperties.annotationType, "precursor",
+ ConfigureMetricsUIPage.AnnotationMetricProperties.annotationName, "RSquared"), true);
+
+ log("Edit the annotation-backed metric's y-axis label (still on same page after cancel)");
+ configureQCMetrics.editAnnotationMetric(metricName, Map.of(
+ ConfigureMetricsUIPage.AnnotationMetricProperties.yAxisLabel, updatedYAxisLabel));
+
+ log("Delete the annotation-backed metric");
+ configureQCMetrics = goToDashboard().getQcSummaryWebPart().clickConfigureQCMetrics();
+ configureQCMetrics.deleteAnnotationMetric(metricName);
+ assertTextNotPresent(metricName);
+ }
+
private void verifyOutlierCount(String replicate, QCPlotsWebPart.MetricType metricType, String count)
{
QCSummaryWebPart qcSummaryWebPart = new PanoramaDashboard(this).getQcSummaryWebPart();
diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSTest.java
index 985b32a14..a18b96277 100644
--- a/test/src/org/labkey/test/tests/targetedms/TargetedMSTest.java
+++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSTest.java
@@ -19,6 +19,7 @@
import org.junit.BeforeClass;
import org.labkey.test.BaseWebDriverTest;
import org.labkey.test.Locator;
+import org.labkey.test.WebDriverWrapper;
import org.labkey.test.ModulePropertyValue;
import org.labkey.test.TestFileUtils;
import org.labkey.test.TestProperties;
@@ -37,9 +38,8 @@
import org.labkey.test.util.LoggedParam;
import org.labkey.test.util.ReflectionUtils;
import org.labkey.test.util.UIContainerHelper;
-import org.openqa.selenium.WebElement;
+import org.labkey.test.util.targetedms.TargetedMSHelper;
-import java.nio.file.Paths;
import java.util.Arrays;
import java.util.List;
@@ -62,6 +62,7 @@ public abstract class TargetedMSTest extends BaseWebDriverTest
protected static final String SAMPLE_FILE_CHROM_INFO = "SampleFileChromInfo.sky.zip";
protected static final String USER = "qcuser@targetedms.test";
private static ConfiguresSite siteConfigurer;
+ protected final TargetedMSHelper _targetedMSHelper = new TargetedMSHelper(this);
protected enum SvgShapes
{
@@ -85,7 +86,7 @@ public enum FolderType {
Experiment
{
@Override
- public void chooseFolderType(TargetedMSTest test)
+ public void chooseFolderType(WebDriverWrapper test)
{
test.click(Locator.radioButtonById("experimentalData")); // click the first radio button - Experimental Data
}
@@ -93,21 +94,21 @@ public void chooseFolderType(TargetedMSTest test)
ExperimentMAM
{
@Override
- public void chooseFolderType(TargetedMSTest test)
+ public void chooseFolderType(WebDriverWrapper test)
{
test.click(Locator.radioButtonById("multiAttributeMethod")); // click the second radio button - Experimental Data
}
}, Library
{
@Override
- public void chooseFolderType(TargetedMSTest test)
+ public void chooseFolderType(WebDriverWrapper test)
{
test.click(Locator.radioButtonById("chromatogramLibrary")); // click the 3rd radio button - Library
}
}, LibraryProtein
{
@Override
- public void chooseFolderType(TargetedMSTest test)
+ public void chooseFolderType(WebDriverWrapper test)
{
test.click(Locator.radioButtonById("chromatogramLibrary")); // click the 3rd radio button - Library
test.click(Locator.checkboxByName("precursorNormalized")); // check the normalization checkbox.
@@ -115,13 +116,13 @@ public void chooseFolderType(TargetedMSTest test)
}, QC
{
@Override
- public void chooseFolderType(TargetedMSTest test)
+ public void chooseFolderType(WebDriverWrapper test)
{
test.click(Locator.radioButtonById("QC")); // click the 4th radio button - QC
}
};
- public abstract void chooseFolderType(TargetedMSTest test);
+ public abstract void chooseFolderType(WebDriverWrapper test);
}
public TargetedMSTest()
@@ -181,10 +182,7 @@ protected void setupFolder(FolderType folderType)
protected void setUpFolder(String folderName, FolderType folderType )
{
- _containerHelper.createProject(folderName, "Panorama");
- waitForElement(Locator.linkContainingText("Save"));
- clickAndWait(Locator.linkContainingText("Next"));
- selectFolderType(folderType);
+ _targetedMSHelper.setupFolder(folderName, folderType);
getSiteConfigurer().configureProject(getProjectName());
}
@@ -227,20 +225,7 @@ protected void importData(@LoggedParam String file, int jobCount, boolean expect
@LogMethod
protected void importData(@LoggedParam String file, int jobCount, boolean expectError, boolean doDbMaintenance)
{
- Locator.XPathLocator importButtonLoc = Locator.lkButton("Process and Import Data");
- WebElement importButton = importButtonLoc.findElementOrNull(getDriver());
- if (null == importButton)
- {
- goToModule("Pipeline");
- importButton = importButtonLoc.findElement(getDriver());
- }
- clickAndWait(importButton);
- String fileName = Paths.get(file).getFileName().toString();
- if (!_fileBrowserHelper.fileIsPresent(fileName))
- _fileBrowserHelper.uploadFile(TestFileUtils.getSampleData("TargetedMS/" + file));
- _fileBrowserHelper.importFile(fileName, "Import Skyline Results");
- waitForText("Skyline document import");
- waitForPipelineJobsToComplete(jobCount, file, expectError);
+ _targetedMSHelper.importData(file, jobCount, expectError);
if (doDbMaintenance)
{
@@ -273,22 +258,32 @@ private void runDbMaintenance()
}
}
- protected void verifyRunSummaryCountsSmallMol(int proteinCount, int peptideCount, int moleculeCount, int precursorCount, int transitionCount, int replicateCount, int calibrationCount, int listCount)
+ protected void verifyRunSummaryCountsSmallMol(int moleculeGroupCount, int proteinCount, int peptideCount, int moleculeCount, int precursorCount, int transitionCount, int replicateCount, int calibrationCount, int listCount)
+ {
+ verifyRunSummaryCounts(0, moleculeGroupCount, proteinCount, peptideCount, moleculeCount, precursorCount, transitionCount, replicateCount, calibrationCount, listCount);
+ }
+
+ protected void verifyRunSummaryCountsPep(int peptideGroupCount, int proteinCount, int peptideCount, int moleculeCount, int precursorCount, int transitionCount, int replicateCount, int calibrationCount, int listCount)
{
- verifyRunSummaryCounts(proteinCount, peptideCount, moleculeCount, precursorCount, transitionCount, replicateCount, calibrationCount, listCount, "molecule lists");
+ verifyRunSummaryCounts(peptideGroupCount, 0, proteinCount, peptideCount, moleculeCount, precursorCount, transitionCount, replicateCount, calibrationCount, listCount);
}
- protected void verifyRunSummaryCountsPep(int proteinCount, int peptideCount, int moleculeCount, int precursorCount, int transitionCount, int replicateCount, int calibrationCount, int listCount)
+ protected void verifyRunSummaryCountsMixed(int proteinGroupCount, int moleculeGroupCount, int proteinCount, int peptideCount, int moleculeCount, int precursorCount, int transitionCount, int replicateCount, int calibrationCount, int listCount)
{
- verifyRunSummaryCounts(proteinCount, peptideCount, moleculeCount, precursorCount, transitionCount, replicateCount, calibrationCount, listCount, "proteins");
+ verifyRunSummaryCounts(proteinGroupCount, moleculeGroupCount, proteinCount, peptideCount, moleculeCount, precursorCount, transitionCount, replicateCount, calibrationCount, listCount);
}
@LogMethod
- protected void verifyRunSummaryCounts(int proteinCount, int peptideCount, int moleculeCount, int precursorCount, int transitionCount,
- int replicateCount, int calibrationCount, int listCount, String peptideGroupLabel)
+ protected void verifyRunSummaryCounts(int proteinGroupCount, int moleculeGroupCount, int proteinCount, int peptideCount, int moleculeCount, int precursorCount, int transitionCount,
+ int replicateCount, int calibrationCount, int listCount)
{
log("Verifying expected summary counts");
- waitForElement(Locator.linkContainingText(proteinCount + " " + peptideGroupLabel));
+ if (proteinGroupCount > 0)
+ waitForElement(Locator.linkContainingText(proteinGroupCount + " protein group" + (proteinGroupCount == 1 ? "" : "s")));
+ if (moleculeGroupCount > 0)
+ assertElementPresent(Locator.linkContainingText(moleculeGroupCount + " molecule list" + (moleculeGroupCount == 1 ? "" : "s")));
+ if (proteinCount > 0)
+ assertElementPresent(Locator.linkContainingText(proteinCount + " protein" + (proteinCount == 1 ? "" : "s")));
if (peptideCount > 0)
{
assertElementPresent(Locator.linkContainingText(peptideCount + " peptides"));
@@ -327,9 +322,7 @@ protected void verifyRunSummaryCounts(int proteinCount, int peptideCount, int mo
@LogMethod
protected void selectFolderType(FolderType folderType) {
- log("Select Folder Type: " + folderType);
- folderType.chooseFolderType(this);
- clickButton("Finish");
+ _targetedMSHelper.selectFolderType(folderType);
}
/** Verify that the comparison plots have been AJAX'd into place */
diff --git a/test/src/org/labkey/test/tests/targetedms/upgrade/TargetedMSUpgradeTest.java b/test/src/org/labkey/test/tests/targetedms/upgrade/TargetedMSUpgradeTest.java
new file mode 100644
index 000000000..8220294af
--- /dev/null
+++ b/test/src/org/labkey/test/tests/targetedms/upgrade/TargetedMSUpgradeTest.java
@@ -0,0 +1,91 @@
+package org.labkey.test.tests.targetedms.upgrade;
+
+import org.junit.Assume;
+import org.junit.Test;
+import org.junit.experimental.categories.Category;
+import org.labkey.remoteapi.query.SelectRowsCommand;
+import org.labkey.remoteapi.query.SelectRowsResponse;
+import org.labkey.test.tests.targetedms.TargetedMSTest.FolderType;
+import org.labkey.test.tests.upgrade.BaseUpgradeTest;
+import org.labkey.test.util.UIContainerHelper;
+import org.labkey.test.util.targetedms.TargetedMSHelper;
+
+import java.util.List;
+import java.util.Map;
+
+import static org.junit.Assert.assertEquals;
+
+/**
+ * Verifies that the targetedms-26.006-26.007 upgrade script correctly populates PeptideGroupCount,
+ * MoleculeGroupCount, and ProteinCount on existing runs after the schema migration.
+ */
+@Category({})
+public class TargetedMSUpgradeTest extends BaseUpgradeTest
+{
+ private static final String SKY_FILE = "smallmol_plus_peptides.sky.zip";
+
+ public TargetedMSUpgradeTest()
+ {
+ setContainerHelper(new UIContainerHelper(this));
+ }
+
+ @Override
+ protected String getProjectName()
+ {
+ return "TargetedMS Upgrade Test";
+ }
+
+ @Override
+ protected void doSetup() throws Exception
+ {
+ TargetedMSHelper helper = new TargetedMSHelper(this);
+ helper.setupFolder(getProjectName(), FolderType.Experiment);
+ helper.importData(SKY_FILE);
+ }
+
+ @Test
+ @EarliestVersion("25.11")
+ public void testPreUpgradeCounts() throws Exception
+ {
+ SelectRowsCommand cmd = new SelectRowsCommand("targetedms", "Runs");
+ cmd.setColumns(List.of("PeptideCount", "SmallMoleculeCount", "ReplicateCount"));
+ SelectRowsResponse response = cmd.execute(createDefaultConnection(), getProjectName());
+
+ List> rows = response.getRows();
+ assertEquals("Expected exactly one run", 1, rows.size());
+ Map run = rows.getFirst();
+ assertEquals("PeptideCount", 44, ((Number) run.get("PeptideCount")).intValue());
+ assertEquals("SmallMoleculeCount", 98, ((Number) run.get("SmallMoleculeCount")).intValue());
+ assertEquals("ReplicateCount", 5, ((Number) run.get("ReplicateCount")).intValue());
+ }
+
+ @Test
+ @EarliestVersion("26.3")
+ public void testPostUpgradeCounts() throws Exception
+ {
+ Assume.assumeFalse("Skipping post-upgrade count checks during setup phase", isUpgradeSetupPhase);
+
+ SelectRowsCommand cmd = new SelectRowsCommand("targetedms", "Runs");
+ cmd.setColumns(List.of("PeptideGroupCount", "MoleculeGroupCount", "ProteinCount"));
+ SelectRowsResponse response = cmd.execute(createDefaultConnection(), getProjectName());
+
+ List> rows = response.getRows();
+ assertEquals("Expected exactly one run", 1, rows.size());
+ Map run = rows.getFirst();
+ assertEquals("PeptideGroupCount", 24, ((Number) run.get("PeptideGroupCount")).intValue());
+ assertEquals("MoleculeGroupCount", 3, ((Number) run.get("MoleculeGroupCount")).intValue());
+ assertEquals("ProteinCount", 24, ((Number) run.get("ProteinCount")).intValue());
+ }
+
+ @Override
+ protected void doCleanup(boolean afterTest)
+ {
+ _containerHelper.deleteProject(getProjectName(), afterTest);
+ }
+
+ @Override
+ public List getAssociatedModules()
+ {
+ return List.of("targetedms");
+ }
+}
diff --git a/test/src/org/labkey/test/util/targetedms/TargetedMSHelper.java b/test/src/org/labkey/test/util/targetedms/TargetedMSHelper.java
new file mode 100644
index 000000000..36797c54e
--- /dev/null
+++ b/test/src/org/labkey/test/util/targetedms/TargetedMSHelper.java
@@ -0,0 +1,68 @@
+package org.labkey.test.util.targetedms;
+
+import org.labkey.test.BaseWebDriverTest;
+import org.labkey.test.Locator;
+import org.labkey.test.TestFileUtils;
+import org.labkey.test.tests.targetedms.TargetedMSTest.FolderType;
+import org.labkey.test.util.LogMethod;
+import org.labkey.test.util.LoggedParam;
+import org.openqa.selenium.WebElement;
+
+import java.nio.file.Paths;
+
+/** Setup and import utilities to share between standard and upgrade tests for TargetedMS */
+public class TargetedMSHelper
+{
+ private final BaseWebDriverTest _test;
+
+ public TargetedMSHelper(BaseWebDriverTest test)
+ {
+ _test = test;
+ }
+
+ public void setupFolder(String projectName, FolderType folderType)
+ {
+ _test._containerHelper.createProject(projectName, "Panorama");
+ _test.waitForElement(Locator.linkContainingText("Save"));
+ _test.clickAndWait(Locator.linkContainingText("Next"));
+ selectFolderType(folderType);
+ }
+
+ @LogMethod
+ public void selectFolderType(@LoggedParam FolderType folderType)
+ {
+ _test.log("Select Folder Type: " + folderType);
+ folderType.chooseFolderType(_test);
+ _test.clickButton("Finish");
+ }
+
+ public void importData(String file)
+ {
+ importData(file, 1);
+ }
+
+ @LogMethod
+ public void importData(@LoggedParam String file, int jobCount)
+ {
+ importData(file, jobCount, false);
+ }
+
+ @LogMethod
+ public void importData(@LoggedParam String file, int jobCount, boolean expectError)
+ {
+ Locator.XPathLocator importButtonLoc = Locator.lkButton("Process and Import Data");
+ WebElement importButton = importButtonLoc.findElementOrNull(_test.getDriver());
+ if (null == importButton)
+ {
+ _test.goToModule("Pipeline");
+ importButton = importButtonLoc.findElement(_test.getDriver());
+ }
+ _test.clickAndWait(importButton);
+ String fileName = Paths.get(file).getFileName().toString();
+ if (!_test._fileBrowserHelper.fileIsPresent(fileName))
+ _test._fileBrowserHelper.uploadFile(TestFileUtils.getSampleData("TargetedMS/" + file));
+ _test._fileBrowserHelper.importFile(fileName, "Import Skyline Results");
+ _test.waitForText("Skyline document import");
+ _test.waitForPipelineJobsToComplete(jobCount, file, expectError);
+ }
+}