JBrowseTest: collapse features by location to find unique (#222)

* JBrowseTest: collapse features by location to find unique

Author: bbimber

jbrowse/src/client/JBrowse/VariantSearch/components/VariantTableWidget.tsx

@@ -211,7 +211,6 @@ const VariantTableWidget = observer(props => {
     }
 
     // Contains all features from the API call once the useEffect finished
-    //const [features, setFeatures] = useState<ExtendedVcfFeature[]>([])
     const [features, setFeatures] = useState<any[]>([])
     const [columns, setColumns] = useState<GridColDef[]>([])
 

jbrowse/test/src/org/labkey/test/tests/external/labModules/JBrowseTest.java

@@ -420,7 +420,7 @@ private void testMessageDisplay()
         waitForJBrowseToLoad();
 
         Actions actions = new Actions(getDriver());
-        WebElement toClick = getDriver().findElements(getVariantWithinTrack("mgap_hg38", "deletion TA -> T")).stream().filter(WebElement::isDisplayed).findFirst().orElseThrow();
+        WebElement toClick = getDriver().findElements(JBrowseTestHelper.getVariantWithinTrack(this, "mgap_hg38", "deletion TA -> T", false)).stream().filter(WebElement::isDisplayed).findFirst().orElseThrow();
         actions.click(toClick).perform();
         waitForElement(Locator.tagContainingText("div", "Aut molestiae temporibus nesciunt."));
     }

jbrowse/test/src/org/labkey/test/tests/external/labModules/JBrowseTestHelper.java

@@ -13,6 +13,7 @@
 import org.labkey.test.util.ext4cmp.Ext4FieldRef;
 import org.labkey.test.util.ext4cmp.Ext4GridRef;
 import org.openqa.selenium.By;
+import org.openqa.selenium.Point;
 import org.openqa.selenium.StaleElementReferenceException;
 import org.openqa.selenium.WebElement;
 
@@ -25,13 +26,19 @@ public class JBrowseTestHelper
     public static final File MGAP_TEST_VCF = new File(TestFileUtils.getLabKeyRoot(), "server/modules/DiscvrLabKeyModules/jbrowse/resources/web/jbrowse/mgap/mGap.v2.1.subset.vcf.gz");
     public static final File GRCH37_GENOME = new File(TestFileUtils.getLabKeyRoot(), "server/modules/DiscvrLabKeyModules/jbrowse/resources/web/jbrowse/mgap/GRCh37_small.fasta");
 
-    public static <T> Collector<T, ?, T> toSingleton() {
+    public static Collector<WebElement, ?, WebElement> toSingleton() {
         return Collectors.collectingAndThen(
                 Collectors.toList(),
                 list -> {
                     if (list.size() != 1) {
-                        throw new IllegalStateException("Expected single element, found: " + list.size());
+                        long uniqueLocations = list.stream().map(WebElement::getLocation).distinct().count();
+                        if (uniqueLocations == 1) {
+                            return list.get(0);
+                        }
+
+                        throw new IllegalStateException("Expected single element, found: " + list.size() + ", " + list.stream().map(WebElement::getLocation).map(Point::toString).collect(Collectors.joining(" / ")));
                     }
+
                     return list.get(0);
                 }
         );
@@ -128,10 +135,19 @@ public static Locator.XPathLocator getTrackLocator(BaseWebDriverTest test, Strin
     }
 
     public static By getVariantWithinTrack(BaseWebDriverTest test, String trackId, String variantText)
+    {
+        return getVariantWithinTrack(test, trackId, variantText, true);
+    }
+
+    public static By getVariantWithinTrack(BaseWebDriverTest test, String trackId, String variantText, boolean appendPolygon)
     {
         Locator.XPathLocator l = getTrackLocator(test, trackId, true);
         test.waitForElementToDisappear(Locator.tagWithText("p", "Loading"));
-        l = l.append(Locator.xpath("//*[name()='text' and contains(text(), '" + variantText + "')]")).notHidden().append("/..");
+        l = l.append(Locator.xpath("//*[name()='text' and contains(text(), '" + variantText + "')]")).notHidden().parent();
+        if (appendPolygon){
+            l = l.append("/*[name()='polygon']");
+        }
+
         test.waitForElement(l);
 
         return By.xpath(l.toXpath());
@@ -153,14 +169,16 @@ public static long getTotalVariantFeatures(BaseWebDriverTest test)
         Locator l = Locator.tagWithAttribute("svg", "data-testid", "svgfeatures").append(Locator.tag("polygon"));
         try
         {
-            return Locator.findElements(test.getDriver(), l).stream().filter(WebElement::isDisplayed).count();
+            // NOTE: JBrowse renders features using multiple blocks per track, and these tracks can redundantly render identical features on top of one another.
+            // Counting unique locations is indirect, but should result in unique features
+            return Locator.findElements(test.getDriver(), l).stream().filter(WebElement::isDisplayed).map(WebElement::getLocation).distinct().count();
         }
         catch (StaleElementReferenceException e)
         {
             test.log("Stale elements, retrying");
             WebDriverWrapper.sleep(5000);
 
-            return Locator.findElements(test.getDriver(), l).stream().filter(WebElement::isDisplayed).count();
+            return Locator.findElements(test.getDriver(), l).stream().filter(WebElement::isDisplayed).map(WebElement::getLocation).distinct().count();
         }
     }
 }