[bot] Merge 26.3 to develop

gradle.properties

@@ -10,7 +10,7 @@ lookfirstSardineVersion=5.13
 
 jettyVersion=12.1.5
 
-seleniumVersion=4.40.0
+seleniumVersion=4.41.0
 
 mockserverNettyVersion=5.15.0
 

src/org/labkey/test/WebDriverWrapper.java

@@ -63,6 +63,7 @@
 import org.labkey.test.util.TextSearcher;
 import org.labkey.test.util.TextSearcher.TextTransformers;
 import org.labkey.test.util.Timer;
+import org.labkey.test.util.selenium.JavascriptExecutorWrapper;
 import org.labkey.test.util.selenium.ScrollUtils;
 import org.labkey.test.util.selenium.WebDriverUtils;
 import org.openqa.selenium.Alert;
@@ -539,11 +540,7 @@ public Object executeScript(@Language("JavaScript") String script, Object... arg
      */
     public <T> T executeScript(@Language("JavaScript") String script, Class<T> expectedResultType, Object... arguments)
     {
-        Object o = executeScript(script, arguments);
-        if (o != null && !expectedResultType.isAssignableFrom(o.getClass()))
-            Assert.fail("Script return wrong type. Expected '" + expectedResultType.getSimpleName() + "'. Got: " + o.getClass().getName() + ". Result: " + o);
-
-        return (T) o;
+        return new JavascriptExecutorWrapper(getDriver()).executeScript(script, expectedResultType, arguments);
     }
 
     /**
@@ -552,20 +549,12 @@ public <T> T executeScript(@Language("JavaScript") String script, Class<T> expec
      */
     public Object executeAsyncScript(@Language("JavaScript") String script, Object... arguments)
     {
-        script = "var callback = arguments[arguments.length - 1];\n" + // See WebDriver documentation for details on injected callback
-                "try {" +
-                script +
-                "} catch (error) { callback(error); }"; // ensure that the callback is invoked when an exception would otherwise prevent it
-        return ((JavascriptExecutor) getDriver()).executeAsyncScript(script, arguments);
+        return new JavascriptExecutorWrapper(getDriver()).executeAsyncScript(script, arguments);
     }
 
     public <T> T executeAsyncScript(@Language("JavaScript") String script, Class<T> expectedResultType, Object... arguments)
     {
-        Object o = executeAsyncScript(script, arguments);
-        if (o != null && !expectedResultType.isAssignableFrom(o.getClass()))
-            Assert.fail("Script return wrong type. Expected '" + expectedResultType.getSimpleName() + "'. Got: " + o.getClass().getName() + ". Result: " + o);
-
-        return (T) o;
+        return new JavascriptExecutorWrapper(getDriver()).executeAsyncScript(script, expectedResultType, arguments);
     }
 
     @LogMethod(quiet = true)

src/org/labkey/test/components/domain/DomainFieldRow.java

@@ -769,6 +769,8 @@ public DomainFieldRow clickRemoveOntologyConcept()
 
     public void setAllowMultipleSelections(Boolean allowMultipleSelections)
     {
+        WebDriverWrapper.waitFor(() -> elementCache().allowMultipleSelectionsCheckbox.isDisplayed(),
+                "Allow Multiple Selections checkbox did not become visible", 2000);
         elementCache().allowMultipleSelectionsCheckbox.set(allowMultipleSelections);
     }
 

src/org/labkey/test/components/ui/grids/ResponsiveGrid.java

@@ -75,7 +75,7 @@ public WebElement getComponentElement()
 
     public Boolean isLoaded()
     {
-        return getComponentElement().isDisplayed() &&
+        return WebElementUtils.checkVisibility(getComponentElement()) &&
                 !Locators.loadingGrid.existsIn(this) &&
                 !Locators.spinner.existsIn(this) &&
                 (Locator.tag("td").existsIn(this) ||

src/org/labkey/test/tests/GpatAssayTest.java

@@ -41,6 +41,7 @@
 import org.labkey.test.util.EscapeUtil;
 import org.labkey.test.util.LogMethod;
 import org.labkey.test.util.LoggedParam;
+import org.labkey.test.util.RReportHelper;
 import org.labkey.test.util.TestDataGenerator;
 import org.labkey.test.util.core.webdav.WebDavUploadHelper;
 import org.openqa.selenium.WebElement;
@@ -72,11 +73,13 @@ public class GpatAssayTest extends BaseWebDriverTest
     private static final String ASSAY_NAME_FNA = "FASTA Assay";
     private static final String ASSAY_NAME_FNA_MULTIPLE = "FASTA Assay - Multiple file upload";
     private static final String ASSAY_NAME_FNA_MULTIPLE_SINGLE_INPUT = "FASTA Assay - Multiple file single input upload";
+    private static final File RTRANSFORM_SCRIPT_FILE_NOOP = TestFileUtils.getSampleData("qc/noopTransform.R");
 
     @BeforeClass
     public static void doSetup()
     {
         GpatAssayTest init = getCurrentTest();
+        new RReportHelper(init).ensureRConfig();
         init._containerHelper.createProject(init.getProjectName(), "Assay");
         init.goToProjectHome();
     }
@@ -256,6 +259,14 @@ private void importFastaGpatAssay(File fnaFile, String assayName)
         clickButton("Save and Finish", defaultWaitForPage);
     }
 
+    // GitHub Issue #875: Optionally add transform scripts in GPAT assay design to test code path with and without transform script
+    private void randomlyAddTransformScript(ReactAssayDesignerPage assayDesignerPage)
+    {
+        boolean shouldAddTransformScript = TestDataGenerator.randomBoolean("whether to add transform script in assay design");
+        if (shouldAddTransformScript)
+            assayDesignerPage.addTransformScript(RTRANSFORM_SCRIPT_FILE_NOOP);
+    }
+
     @LogMethod
     private ReactAssayDesignerPage startCreateGpatAssay(File dataFile, @LoggedParam String assayName)
     {
@@ -265,9 +276,9 @@ private ReactAssayDesignerPage startCreateGpatAssay(File dataFile, @LoggedParam
         _fileBrowserHelper.importFile(dataFile.getName(), "Create New Standard Assay Design");
 
         ReactAssayDesignerPage assayDesignerPage = new ReactAssayDesignerPage(getDriver());
-
         if (assayName != null)
             assayDesignerPage.setName(assayName);
+        randomlyAddTransformScript(assayDesignerPage);
         return assayDesignerPage;
     }
 

src/org/labkey/test/util/TestDataGenerator.java

@@ -800,7 +800,15 @@ public String randomDateString(String dateFormat, Date min, Date max)
 
     public static boolean randomBoolean()
     {
-        return ThreadLocalRandom.current().nextBoolean();
+        return randomBoolean(null);
+    }
+
+    public static boolean randomBoolean(@Nullable String message)
+    {
+        boolean value = ThreadLocalRandom.current().nextBoolean();
+        if (message != null)
+            TestLogger.log("Generated random boolean value for %s: %s".formatted(message, value));
+        return value;
     }
 
     private @NotNull List<String> getFieldsForFile()

src/org/labkey/test/util/data/TestDataUtils.java

@@ -581,14 +581,13 @@ public static List<List<String>> readRowsFromFile(File file, CSVFormat format) t
     public static List<String> parseMultiValueText(String multiValueString) throws IOException
     {
         CSVFormat format = CSVFormat.RFC4180.builder()
-                .setIgnoreSurroundingSpaces(true).get();
+                .setIgnoreSurroundingSpaces(true).setTrim(true).get();
         try (CSVParser parser = format.parse(new StringReader(multiValueString)))
         {
             List<CSVRecord> records = parser.getRecords();
-            List<List<String>> list = records.stream().map(CSVRecord::toList).toList();
-            if (list.size() != 1)
+            if (records.size() != 1)
                 throw new IllegalArgumentException("Invalid multi-value text string: " + multiValueString);
-            return list.getFirst();
+            return records.getFirst().toList();
         }
     }
 

src/org/labkey/test/util/selenium/JavascriptExecutorWrapper.java

@@ -0,0 +1,85 @@
+package org.labkey.test.util.selenium;
+
+import org.intellij.lang.annotations.Language;
+import org.jetbrains.annotations.Nullable;
+import org.openqa.selenium.JavascriptExecutor;
+import org.openqa.selenium.ScriptKey;
+import org.openqa.selenium.WebDriver;
+
+import java.util.Set;
+
+public class JavascriptExecutorWrapper implements JavascriptExecutor
+{
+    private final JavascriptExecutor _wrappedExecutor;
+
+    public JavascriptExecutorWrapper(WebDriver driver)
+    {
+        _wrappedExecutor = (JavascriptExecutor) driver;
+    }
+
+    @Override
+    public @Nullable Object executeScript(@Language("JavaScript") String script, @Nullable Object... args)
+    {
+        return _wrappedExecutor.executeScript(script, args);
+    }
+
+    @Override
+    public @Nullable Object executeScript(ScriptKey key, @Nullable Object... args)
+    {
+        return _wrappedExecutor.executeScript(key, args);
+    }
+
+    /**
+     * Wrapper for executing JavaScript through WebDriver and verifying return type.
+     * @param <T> See {@link JavascriptExecutor#executeScript(java.lang.String, java.lang.Object...)} for valid return types
+     */
+    public <T> @Nullable T executeScript(@Language("JavaScript") String script, Class<T> expectedResultType, @Nullable Object... arguments)
+    {
+        return verifyType(expectedResultType, executeScript(script, arguments));
+    }
+
+    /**
+     * Wrapper for synchronous execution of asynchronous JavaScript. This wrapper extracts the 'callback' from the argument list
+     * See {@link JavascriptExecutor#executeAsyncScript(java.lang.String, java.lang.Object...)} for details
+     */
+    @Override
+    public @Nullable Object executeAsyncScript(@Language("JavaScript") String script, @Nullable Object... arguments)
+    {
+        script = "var callback = arguments[arguments.length - 1];\n" + // See WebDriver documentation for details on injected callback
+                "try {" +
+                script +
+                "} catch (error) { callback(error); }"; // ensure that the callback is invoked when an exception would otherwise prevent it
+        return _wrappedExecutor.executeAsyncScript(script, arguments);
+    }
+
+    public <T> @Nullable T executeAsyncScript(@Language("JavaScript") String script, Class<T> expectedResultType, @Nullable Object... arguments)
+    {
+        return verifyType(expectedResultType, executeAsyncScript(script, arguments));
+    }
+
+    private <T> @Nullable T verifyType(Class<T> expectedResultType, @Nullable Object o)
+    {
+        if (o != null && !expectedResultType.isAssignableFrom(o.getClass()))
+            throw new IllegalStateException("Script return wrong type. Expected '" + expectedResultType.getName() + "'. Got: " + o.getClass().getName() + ". Result: " + o);
+
+        return (T) o;
+    }
+
+    @Override
+    public Set<ScriptKey> getPinnedScripts()
+    {
+        return _wrappedExecutor.getPinnedScripts();
+    }
+
+    @Override
+    public void unpin(ScriptKey key)
+    {
+        _wrappedExecutor.unpin(key);
+    }
+
+    @Override
+    public ScriptKey pin(@Language("JavaScript") String script)
+    {
+        return _wrappedExecutor.pin(script);
+    }
+}

src/org/labkey/test/util/selenium/WebDriverUtils.java

@@ -25,6 +25,8 @@
 import org.openqa.selenium.WrapsDriver;
 import org.openqa.selenium.WrapsElement;
 
+import java.util.Objects;
+
 public abstract class WebDriverUtils
 {
     /**
@@ -74,6 +76,17 @@ public static WebDriver extractWrappedDriver(Object peeling)
             return null;
     }
 
+    /**
+     * Extract a WebDriver instance from an arbitrarily wrapped object and the JavascriptExecutor tied to it.
+     *
+     * @param object Object that wraps a WebDriver. Typically, a Component, SearchContext, or WebElement
+     * @return JavascriptExecutor instance
+     */
+    public static JavascriptExecutorWrapper getJavascriptExecutor(Object object)
+    {
+        return Objects.requireNonNull(new JavascriptExecutorWrapper(extractWrappedDriver(object)), () -> "No WebDriver found in " + object.getClass());
+    }
+
     /**
      * Attempts to get alert text from an {@link UnhandledAlertException}. If exception does not supply the alert text,
      * attempt to get it from the alert directly (requires {@link org.openqa.selenium.UnexpectedAlertBehaviour#IGNORE}).

src/org/labkey/test/util/selenium/WebElementUtils.java

@@ -1,13 +1,17 @@
 package org.labkey.test.util.selenium;
 
 import org.intellij.lang.annotations.Language;
+import org.labkey.test.selenium.LazyWebElement;
 import org.openqa.selenium.JavascriptExecutor;
 import org.openqa.selenium.NoSuchElementException;
+import org.openqa.selenium.StaleElementReferenceException;
 import org.openqa.selenium.WebDriverException;
 import org.openqa.selenium.WebElement;
 
 import java.util.Collections;
 import java.util.List;
+import java.util.Objects;
+import java.util.Optional;
 
 import static org.labkey.test.Locator.NBSP;
 
@@ -93,6 +97,29 @@ public static String getTextNodeWithin(WebElement element)
      */
     public static String getTextContent(WebElement element)
     {
-        return element.getDomProperty("textContent").replace(NBSP, " ");
+        return Optional.ofNullable(element.getDomProperty("textContent")).map(s -> s.replace(NBSP, " ")).orElse(null);
+    }
+
+    /**
+     * Determines whether the specified element is visible. {@link WebElement#isDisplayed()} might return false if the
+     * element is out the viewport and scrolling is disabled due to a modal dialog.<br>
+     * TODO: Consider moving to {@link LazyWebElement#isDisplayed()}
+     *
+     * @param element element to inspect
+     * @return true if the element is visible, false otherwise
+     */
+    public static boolean checkVisibility(WebElement element)
+    {
+        try
+        {
+            return element.isDisplayed() ||
+                    Objects.requireNonNullElse(WebDriverUtils.getJavascriptExecutor(element)
+                            .executeScript("return arguments[0].checkVisibility();", Boolean.class, element),
+                            false);
+        }
+        catch (NoSuchElementException | StaleElementReferenceException e)
+        {
+            return false;
+        }
     }
 }