Improve QC folder plot controls (#1120)

Author: labkey-jeckels

resources/views/configureQCGroups.html

@@ -60,12 +60,12 @@
                     LABKEY.QueryWebPart.standardButtons.print,
                     LABKEY.QueryWebPart.standardButtons.pageSize,
                     {
-                        text: 'Mark As Included',
+                        text: 'Include',
                         requiresSelection: 'true',
                         handler: markPrecursorAsIncludedHandler
                     },
                     {
-                        text: 'Mark As Excluded',
+                        text: 'Exclude',
                         requiresSelection: 'true',
                         handler: markPrecursorAsExcludedHandler
                     }

src/org/labkey/targetedms/view/qcTrendPlotReport.jsp

@@ -56,7 +56,8 @@
     String plotPanelId = "tiledPlotPanel-" + uid;
     String plotPaginationPanelId = "plotPaginationPanel-" + uid;
 %>
-
+<!-- Help ExtJS plot controls reliably grab the width they need -->
+<div style="height: 1px; width: 1250px;"></div>
 <div id="<%=h(reportPanelId)%>"></div>
 <div id="<%=h(plotPaginationPanelId)%>" class="plotPaginationHeaderPanel"></div>
 <div id="<%=h(plotPanelId)%>" class="tiledPlotPanel"></div>

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

@@ -20,8 +20,8 @@
 import org.labkey.test.Locators;
 import org.labkey.test.WebDriverWrapper;
 import org.labkey.test.components.BodyWebPart;
-import org.labkey.test.components.ext4.Checkbox;
 import org.labkey.test.components.ext4.ComboBox;
+import org.labkey.test.components.ext4.RadioButton;
 import org.labkey.test.components.ext4.Window;
 import org.labkey.test.util.Ext4Helper;
 import org.labkey.test.util.LogMethod;
@@ -252,22 +252,44 @@ public Set<QCPlotType> getCurrentQCPlotTypes()
 
     public void setGroupXAxisValuesByDate(boolean check)
     {
-        if (elementCache().groupedXCheckbox.get() != check)
+        if (isGroupXAxisValuesByDateChecked() != check)
         {
-            doAndWaitForUpdate(() -> elementCache().groupedXCheckbox.set(check));
+            if (check)
+                doAndWaitForUpdate(() -> elementCache().xAxisGroupingDateRadio.check());
+            else
+                doAndWaitForUpdate(() -> elementCache().xAxisGroupingReplicateRadio.check());
         }
     }
 
     public boolean isGroupXAxisValuesByDateChecked()
     {
-        return elementCache().groupedXCheckbox.isChecked();
+        try
+        {
+            return elementCache().xAxisGroupingDateRadio.isSelected();
+        }
+        catch (NoSuchElementException | StaleElementReferenceException e)
+        {
+            // Fallback: if radios are not present yet, assume unchecked
+            return false;
+        }
     }
 
     public void setShowAllPeptidesInSinglePlot(boolean check)
     {
-        if (elementCache().singlePlotCheckbox.get() != check)
+        // 'check' means show all series combined in a single plot
+        try
         {
-            doAndWaitForUpdate(() -> elementCache().singlePlotCheckbox.set(check));
+            if (isShowAllPeptidesInSinglePlotChecked() != check)
+            {
+                if (check)
+                    doAndWaitForUpdate(() -> elementCache().plotsCombinedRadio.check());
+                else
+                    doAndWaitForUpdate(() -> elementCache().plotsPerPrecursorRadio.check());
+            }
+        }
+        catch (NoSuchElementException | StaleElementReferenceException e)
+        {
+            // Fallback: ignore if control not present yet
         }
     }
 
@@ -282,32 +304,63 @@ public void setShowAllPeptidesInSinglePlot(boolean check, int expectedPlotCount)
 
     public void setShowExcludedPoints(boolean check)
     {
-        elementCache().showExcludedCheckbox.set(check);
+        if (check)
+        {
+            elementCache().excludedReplicatesShow.check();
+        }
+        else
+        {
+            elementCache().excludedReplicatesHide.check();
+        }
     }
 
     public boolean isShowExcludedPointsChecked()
     {
-        return elementCache().showExcludedCheckbox.isChecked();
+        return elementCache().excludedReplicatesShow.isChecked();
     }
 
     public void setShowReferenceGuideSet(boolean check)
     {
-        elementCache().showReferenceGuideSet.set(check);
+        if (isShowReferenceGuideSetChecked() != check)
+        {
+            if (check)
+            {
+                elementCache().referenceGuideSetShow.check();
+            }
+            else
+            {
+                elementCache().referenceGuideSetHide.check();
+            }
+        }
     }
 
     public void setShowExcludedPrecursors(boolean check)
     {
-        elementCache().showExcludedPrecursors.set(check);
+        if (check)
+        {
+            elementCache().excludedPrecursorsShow.check();
+        }
+        else
+        {
+            elementCache().excludedPrecursorsHide.check();
+        }
     }
 
     public boolean isShowReferenceGuideSetChecked()
     {
-        return elementCache().showReferenceGuideSet.isChecked();
+        return elementCache().referenceGuideSetShow.isChecked();
     }
 
     public boolean isShowAllPeptidesInSinglePlotChecked()
     {
-        return elementCache().singlePlotCheckbox.isChecked();
+        try
+        {
+            return elementCache().plotsCombinedRadio.isSelected();
+        }
+        catch (NoSuchElementException | StaleElementReferenceException e)
+        {
+            return false;
+        }
     }
 
     public QCPlotsWebPart saveAsDefaultView()
@@ -323,11 +376,6 @@ public QCPlotsWebPart revertToDefaultView()
         return this;
     }
 
-    public void applyRange()
-    {
-        doAndWaitForUpdate(() -> elementCache().applyRangeButton.click());
-    }
-
     public void waitForPlots(Integer plotCount)
     {
         if (plotCount > 0)
@@ -341,6 +389,11 @@ public void waitForPlots(Integer plotCount)
         }
     }
 
+    public boolean isCombinedPlotControlVisible()
+    {
+        return elementCache().plotsCombinedRadio.isDisplayed();
+    }
+
     public List<QCPlot> getPlots()
     {
         return elementCache().findSeriesPanels().stream().map(QCPlot::new).toList();
@@ -374,7 +427,7 @@ public void filterQCPlotsToInitialData(int expectedPlotCount, boolean resetForm)
             resetInitialQCPlotFields();
         }
 
-        filterQCPlots("2013-08-09", "2013-08-27", expectedPlotCount);
+        filterQCPlots("2013-08-09", "2013-08-27", resetForm);
     }
 
     @LogMethod
@@ -391,13 +444,18 @@ public void resetInitialQCPlotFields()
     }
 
     @LogMethod
-    public void filterQCPlots(@LoggedParam String startDate, @LoggedParam String endDate, int expectedPlotCount)
+    public void filterQCPlots(@LoggedParam String startDate, @LoggedParam String endDate, boolean waitForPlotsToRefresh)
     {
         setDateRangeOffset(DateRangeOffset.CUSTOM);
         setStartDate(startDate);
-        setEndDate(endDate);
-        applyRange();
-        waitForPlots(expectedPlotCount);
+        if (waitForPlotsToRefresh)
+        {
+            doAndWaitForUpdate(() -> setEndDate(endDate));
+        }
+        else
+        {
+            setEndDate(endDate);
+        }
     }
 
     public int getGuideSetTrainingRectCount()
@@ -871,17 +929,24 @@ public class Elements extends BodyWebPart<?>.ElementCache
 
         ComboBox qcPlotTypeCombo = new ComboBox.ComboBoxFinder(getDriver()).withIdPrefix("qc-plot-type-with-y-options")
                 .findWhenNeeded(this).setMatcher(Ext4Helper.TextMatchTechnique.CONTAINS).setMultiSelect(true);
-        Checkbox groupedXCheckbox = new Checkbox(Locator.css("#grouped-x-field input")
-                .findWhenNeeded(this).withTimeout(WAIT_FOR_JAVASCRIPT));
-        Checkbox singlePlotCheckbox = new Checkbox(Locator.css("#peptides-single-plot input")
-                .findWhenNeeded(this).withTimeout(WAIT_FOR_JAVASCRIPT));
-        Checkbox showExcludedCheckbox = new Checkbox(Locator.css("#show-excluded-points input")
-                .findWhenNeeded(this).withTimeout(WAIT_FOR_JAVASCRIPT));
-        Checkbox showReferenceGuideSet = new Checkbox(Locator.css("#show-oorange-gs input")
-                .findWhenNeeded(this).withTimeout(WAIT_FOR_JAVASCRIPT));
-        Checkbox showExcludedPrecursors = new Checkbox(Locator.css("#show-excluded-precursors input")
-                .findWhenNeeded(this).withTimeout(WAIT_FOR_JAVASCRIPT));
+        WebElement groupedXPerReplicate = Locator.css("#grouped-x-field input[value=replicate]").findWhenNeeded(this);
+
+        RadioButton xAxisGroupingReplicateRadio = new RadioButton.RadioButtonFinder().withLabel("per replicate").findWhenNeeded(getDriver());
+        RadioButton xAxisGroupingDateRadio = new RadioButton.RadioButtonFinder().withLabel("per date").findWhenNeeded(getDriver());
+
+        RadioButton plotsCombinedRadio = new RadioButton.RadioButtonFinder().withLabel("combined").findWhenNeeded(getDriver());
+        RadioButton plotsPerPrecursorRadio = new RadioButton.RadioButtonFinder().withLabel("per precursor").findWhenNeeded(getDriver());
+
+        // These have the same label as another group, but are first in the page
+        RadioButton excludedReplicatesShow = new RadioButton.RadioButtonFinder().withLabel("show").findWhenNeeded(getDriver());
+        RadioButton excludedReplicatesHide = new RadioButton.RadioButtonFinder().withLabel("hide").findWhenNeeded(getDriver());
+
+        // Note that these two won't work with the isChecked() call but they have the same labels as the ones above so we can't simply check by label
+        RadioButton excludedPrecursorsShow = new RadioButton(Locator.id("excluded-precursors-show").findWhenNeeded(getDriver()));
+        RadioButton excludedPrecursorsHide = new RadioButton(Locator.id("excluded-precursors-hide").findWhenNeeded(getDriver()));
 
+        RadioButton referenceGuideSetShow = new RadioButton.RadioButtonFinder().withLabel("always show").findWhenNeeded(getDriver());
+        RadioButton referenceGuideSetHide = new RadioButton.RadioButtonFinder().withLabel("when in date range").findWhenNeeded(getDriver());
 
         WebElement plotPanel = Locator.css("div.tiledPlotPanel").findWhenNeeded(this);
         WebElement paginationPanel = Locator.css("div.plotPaginationHeaderPanel").findWhenNeeded(this);

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

@@ -128,9 +128,9 @@ private void excludePeptideOrMolecule(String folderName, int rowIndex, String ac
         DataRegionTable table = gotoIncludeExcludeMenu();
         table.checkCheckbox(rowIndex);
         if (action.equals("Excluded"))
-            table.doAndWaitForUpdate(() -> table.clickHeaderButton("Mark As Excluded"));
+            table.doAndWaitForUpdate(() -> table.clickHeaderButton("Exclude"));
         else
-            table.doAndWaitForUpdate(() -> table.clickHeaderButton("Mark As Included"));
+            table.doAndWaitForUpdate(() -> table.clickHeaderButton("Include"));
         checker().withScreenshot("MarkedAsColumnUpdate_" + folderName).verifyEquals("Marked As column not updated with selection of action", action, table.getDataAsText(rowIndex, "markedAs"));
 
         log("Verifying targetedms.ExcludedPrecursors table gets updated with action");

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

@@ -153,6 +153,6 @@ private void excludePrecursors(String projectName, int rowNum)
         qcSummaryWebPart.clickMenuItem("Configure Included and Excluded Precursors");
         DataRegionTable table = new DataRegionTable.DataRegionFinder(getDriver()).waitFor();
         table.checkCheckbox(rowNum);
-        table.clickHeaderButton("Mark As Excluded");
+        table.clickHeaderButton("Exclude");
     }
 }

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

@@ -153,7 +153,7 @@ public void testLinkExperimentalQC()
 
         String testStartDate = "2013-08-18";
         String testEndDate = "2013-08-27";
-        qcPlotsWebPart.filterQCPlots(testStartDate, testEndDate, 7);
+        qcPlotsWebPart.filterQCPlots(testStartDate, testEndDate, true);
 
         checker().verifyTrue("The graph is not divided by line separator",
                 isElementPresent(Locator.tagWithAttribute("line", "class", "separator")));

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

@@ -33,7 +33,7 @@ public abstract class TargetedMSIrtTest extends TargetedMSTest
     private static final String SCHEMA = "targetedms";
     private static final String QUERY = "iRTPeptide";
 
-    // All tests use varations of this test dataset.
+    // All tests use variations of this test dataset.
     protected static final String SKY_FILE = "iRT Human+Standard Calibrate.zip";
     protected static final int PEPTIDE_COUNT = 716;
     protected static final double DELTA = 0.00001;

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

@@ -76,7 +76,7 @@ public void testHeatMapColorAndValues()
         qcPlotsWebPart = new PanoramaDashboard(this).getQcPlotsWebPart();
         qcPlotsWebPart.waitForReady();
         assertEquals("Date Range Offset not set to default value", QCPlotsWebPart.DateRangeOffset.LAST_7_DAYS, qcPlotsWebPart.getCurrentDateRangeOffset());
-        qcPlotsWebPart.filterQCPlots("2013-08-10", "2013-08-15", 7);
+        qcPlotsWebPart.filterQCPlots("2013-08-10", "2013-08-15", true);
 
         // Now navigate through the link instead of the custom tab and webpart
         waitAndClickAndWait(Locator.linkContainingText("View all 47 replicates"));

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

@@ -205,9 +205,10 @@ public void testGuideSetPlotDisplay()
         qcPlotsWebPart.setGroupXAxisValuesByDate(false);
 
         // filter plot by start/end date to check reference points without training points in view
-        qcPlotsWebPart.filterQCPlots("2013-08-19", "2013-08-19", PRECURSORS.length);
+        qcPlotsWebPart.filterQCPlots("2013-08-19", "2013-08-19", true);
         shapeCounts = new ArrayList<>();
         shapeCounts.add(Pair.of(SvgShapes.CIRCLE.getPathPrefix(), 14));
+        qcPlotsWebPart = new QCPlotsWebPart(getDriver());
         verifyGuideSetRelatedElementsForPlots(qcPlotsWebPart, 0, shapeCounts, 2);
     }
 

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

@@ -63,7 +63,6 @@
 import static org.labkey.test.components.targetedms.QCPlotsWebPart.QCPlotType.MetricValue;
 import static org.labkey.test.components.targetedms.QCPlotsWebPart.QCPlotType.MovingRange;
 import static org.labkey.test.components.targetedms.QCPlotsWebPart.QCPlotType.TrailingCV;
-import static org.labkey.test.components.targetedms.QCPlotsWebPart.QCPlotType.TrailingMean;
 import static org.labkey.test.util.PermissionsHelper.READER_ROLE;
 
 @Category({})
@@ -190,6 +189,9 @@ private void doInit()
     public void preTest()
     {
         goToProjectHome();
+        PanoramaDashboard qcDashboard = new PanoramaDashboard(this);
+        QCPlotsWebPart qcPlotsWebPart = qcDashboard.getQcPlotsWebPart();
+        qcPlotsWebPart.revertToDefaultView();
     }
 
     @Test
@@ -346,7 +348,7 @@ public void testQCPlotInputsPersistence()
         qcPlotsWebPart.setScale(QCPlotsWebPart.Scale.PERCENT_OF_MEAN);
         qcPlotsWebPart.setGroupXAxisValuesByDate(true);
         qcPlotsWebPart.setShowAllPeptidesInSinglePlot(true, 1);
-        qcPlotsWebPart.filterQCPlots(testDateStr, testDateStr, 1);
+        qcPlotsWebPart.filterQCPlots(testDateStr, testDateStr, true);
         int count = qcPlotsWebPart.getPointElements("d", SvgShapes.CIRCLE.getPathPrefix(), true).size();
         assertEquals("Unexpected number of points for '" + testDateStr + "'", 21, count);
 
@@ -543,10 +545,10 @@ public void testBadPlotDateRange()
         QCPlotsWebPart qcPlotsWebPart = qcDashboard.getQcPlotsWebPart();
         qcPlotsWebPart.filterQCPlotsToInitialData(PRECURSORS.length, true);
 
-        qcPlotsWebPart.filterQCPlots("2014-08-09", "2014-08-27", 0);
-
-        // reset to avoid test case dependency
-        qcPlotsWebPart.resetInitialQCPlotFields();
+        qcPlotsWebPart.filterQCPlots("2015-08-09", "2014-08-27", false);
+        waitForText("Please enter an end date that does not occur before the start date.");
+        qcPlotsWebPart.filterQCPlots("2014-08-09", "2014-08-27", false);
+        waitForText("There were no records found");
     }
 
     @Test
@@ -697,10 +699,10 @@ public void testRunScopedMetric()
         String ticPlotSVGText = qcPlotsWebPart.getSVGPlotText("precursorPlot0");
         assertFalse(ticPlotSVGText.isEmpty());
 
-        log("Verifying Show All Series Checkbox");
-        assertElementNotVisible(Locator.tagContainingText("label", "Show All Series in a Single Plot"));
+        log("Verifying combined/per-precursor plot controls");
+        assertFalse(qcPlotsWebPart.isCombinedPlotControlVisible());
         qcPlotsWebPart.setMetric1Type(QCPlotsWebPart.MetricType.RETENTION);
-        assertElementVisible(Locator.tagContainingText("label", "Show All Series in a Single Plot"));
+        assertTrue(qcPlotsWebPart.isCombinedPlotControlVisible());
 
         log("Verifying tic_area information in hover plot");
         qcPlotsWebPart.setMetric1Type(QCPlotsWebPart.MetricType.TIC_AREA);