[bot] Fast-forward for 26.3.0

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/BaseWebDriverTest.java

@@ -22,6 +22,7 @@
 import org.apache.commons.lang3.time.FastDateFormat;
 import org.apache.commons.lang3.tuple.ImmutablePair;
 import org.apache.commons.lang3.tuple.Pair;
+import org.apache.hc.core5.http.HttpStatus;
 import org.awaitility.Awaitility;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
@@ -2734,6 +2735,15 @@ private File clickExportImageIcon(String chartParentCls, int chartIndex, Locator
         }
     }
 
+    public void verifyImagePopupInGrid(File imageFile)
+    {
+        mouseOver(Locator.xpath("//img[contains(@title, '" + imageFile.getName() + "')]"));
+        longWait().until(ExpectedConditions.visibilityOfElementLocated(By.cssSelector("#helpDiv")));
+        String src = Locator.xpath("//div[@id='helpDiv']//img[contains(@src, 'download')]").findElement(getDriver()).getAttribute("src");
+        assertTrue("Wrong image in popup: " + src, src.contains(imageFile.getName()));
+        assertEquals("Bad response from image pop-up", HttpStatus.SC_OK, WebTestHelper.getHttpResponse(src).getResponseCode());
+    }
+
     public List<Map<String, Object>> loadTsv(File tsv)
     {
         try (TabLoader loader = new TabLoader(tsv, true))

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/list/ManageListsGrid.java

@@ -53,11 +53,30 @@ public File exportSelectedLists()
 
     public BeginPage deleteSelectedLists()
     {
-        clickHeaderButtonAndWait("Delete");
+        if (getHeaderButton("Delete").getAttribute("class").contains("labkey-down-arrow"))
+            clickHeaderMenu("Delete", true, "Delete List");
+        else
+            clickHeaderButtonAndWait("Delete");
+
         ConfirmDeletePage confirmPage = new ConfirmDeletePage(getDriver());
         return confirmPage.confirmDelete();
     }
 
+    public BeginPage deleteAllDataFromSelectedLists()
+    {
+        clickHeaderMenu("Delete", true, "Delete All Data from List");
+        ConfirmDeletePage confirmPage = new ConfirmDeletePage(getDriver(), "Confirm Delete All Data");
+        return confirmPage.confirmDelete();
+    }
+
+    public ManageListsGrid selectLists(List<String> listNames)
+    {
+        for (String listName : listNames)
+            checkCheckbox(getRowIndex("Name", listName));
+
+        return this;
+    }
+
     public List<String> getListNames()
     {
         return getColumnDataAsText("Name");

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/pages/list/ConfirmDeletePage.java

@@ -8,9 +8,17 @@
 
 public class ConfirmDeletePage extends LabKeyPage<ConfirmDeletePage.ElementCache>
 {
+    private String _deleteBtnText;
+
     public ConfirmDeletePage(WebDriver driver)
+    {
+        this(driver, "Confirm Delete");
+    }
+
+    public ConfirmDeletePage(WebDriver driver, String deleteBtnText)
     {
         super(driver);
+        _deleteBtnText = deleteBtnText;
     }
 
     public BeginPage confirmDelete()
@@ -27,6 +35,6 @@ protected ElementCache newElementCache()
 
     protected class ElementCache extends LabKeyPage<?>.ElementCache
     {
-        WebElement deleteButton = Locator.lkButton("Confirm Delete").findWhenNeeded(this);
+        WebElement deleteButton = Locator.lkButton(_deleteBtnText == null ? "Confirm Delete" : _deleteBtnText).findWhenNeeded(this);
     }
 }

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

@@ -36,6 +36,7 @@
 import static org.labkey.test.params.FieldDefinition.DOMAIN_TRICKY_CHARACTERS;
 import static org.labkey.test.util.PermissionsHelper.EDITOR_ROLE;
 import static org.labkey.test.util.PermissionsHelper.READER_ROLE;
+import static org.labkey.test.util.PermissionsHelper.SEE_AUDIT_LOG_SITE_ROLE;
 
 /**
  * @deprecated TODO: Move shared functionality to a Helper class
@@ -209,8 +210,8 @@ protected void setupEnvironment()
 
         //add a PI user to that group
         permissionsHelper.addUserToProjGroup(TEST_ASSAY_USR_PI1, getProjectName(), TEST_ASSAY_GRP_PIS);
-        // give the PI user "CanSeeAuditLog" permission
-        permissionsHelper.setSiteRoleUserPermissions(TEST_ASSAY_USR_PI1, "See Audit Log Events");
+        // give the PI user site "CanSeeAuditLog" permission
+        permissionsHelper.setSiteRoleUserPermissions(TEST_ASSAY_USR_PI1, SEE_AUDIT_LOG_SITE_ROLE);
 
         //add a lab tech user to the Users group
         permissionsHelper.addUserToProjGroup(TEST_ASSAY_USR_TECH1, getProjectName(), TEST_ASSAY_GRP_USERS);

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

@@ -47,6 +47,7 @@
 import org.labkey.test.util.Log4jUtils;
 import org.labkey.test.util.PermissionsHelper;
 import org.labkey.test.util.PortalHelper;
+import org.labkey.test.util.SearchHelper;
 import org.labkey.test.util.UIUserHelper;
 
 import java.io.BufferedReader;
@@ -64,11 +65,13 @@
 import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertTrue;
 import static org.junit.Assert.fail;
+import static org.labkey.test.util.PasswordUtil.getUsername;
 import static org.labkey.test.util.PermissionsHelper.AUTHOR_ROLE;
 import static org.labkey.test.util.PermissionsHelper.EDITOR_ROLE;
 import static org.labkey.test.util.PermissionsHelper.FOLDER_ADMIN_ROLE;
 import static org.labkey.test.util.PermissionsHelper.PROJECT_ADMIN_ROLE;
-import static org.labkey.test.util.PasswordUtil.getUsername;
+import static org.labkey.test.util.PermissionsHelper.SEE_AUDIT_LOG_FOLDER_ROLE;
+import static org.labkey.test.util.PermissionsHelper.SEE_AUDIT_LOG_SITE_ROLE;
 
 @Category({Daily.class, Hosting.class})
 @BaseWebDriverTest.ClassTimeout(minutes = 9)
@@ -79,21 +82,18 @@ public class AuditLogTest extends BaseWebDriverTest
     public static final String QUERY_UPDATE_EVENT = "Query update events";
     public static final String PROJECT_AUDIT_EVENT = "Project and Folder events";
     public static final String ASSAY_AUDIT_EVENT = "Link to Study events";
+    public static final String COMMENT_COLUMN = "Comment";
 
     private static final String AUDIT_TEST_USER = "audit_user1@auditlog.test";
     private static final String AUDIT_TEST_USER2 = "audit_user2@auditlog.test";
     private static final String AUDIT_TEST_USER3 = "audit_user3@auditlog.test";
-
     private static final String AUDIT_SECURITY_GROUP = "Testers";
-
     private static final String AUDIT_TEST_PROJECT = "AuditVerifyTest";
     private static final String AUDIT_DETAILED_TEST_PROJECT = "AuditDetailedLogTest";
     private static final String AUDIT_TEST_SUBFOLDER = "AuditVerifyTest_Subfolder";
     private static final String AUDIT_PROPERTY_EVENTS_PROJECT = "AuditDomainPropertyEvents";
-
-    final String DOMAIN_PROPERTY_LOG_NAME = "Domain property events";
-
-    public static final String COMMENT_COLUMN = "Comment";
+    private static final String DOMAIN_PROPERTY_LOG_NAME = "Domain property events";
+    private static final String SEARCH_TERM = "doesn't matter";
 
     private final ApiPermissionsHelper permissionsHelper = new ApiPermissionsHelper(this);
     private final AuditLogHelper _auditLogHelper = new AuditLogHelper(this);
@@ -377,19 +377,37 @@ protected void canSeeAuditLogTest()
         createUserWithPermissions(AUDIT_TEST_USER, AUDIT_TEST_PROJECT, EDITOR_ROLE);
         createUserWithPermissions(AUDIT_TEST_USER2, AUDIT_TEST_PROJECT, PROJECT_ADMIN_ROLE);
 
+        // Do a search to ensure an audit entry in /home
+        clickProject("Home");
+        new SearchHelper(this).searchFor(SEARCH_TERM);
+        goToProjectHome();
+
         // signed in as an admin so we should see rows here
-        verifyAuditQueries(true);
+        verifyAuditQueries(true, getProjectName());
 
         // signed in as an editor should not show any rows for audit query links
         impersonate(AUDIT_TEST_USER);
-        verifyAuditQueries(false);
+        verifyAuditQueries(false, getProjectName());
+        verifyAuditQueries(false, "Home");
+        stopImpersonating();
+
+        // Grant the "See Audit Log Events" folder role to our audit user in the project and verify we see audit
+        // information in this project but not /Home. We pass the fully qualified classnames in the next few calls to
+        // disambiguate the root role from the folder role.
+        permissionsHelper.addMemberToRole(AUDIT_TEST_USER, SEE_AUDIT_LOG_FOLDER_ROLE, PermissionsHelper.MemberType.user, getProjectName());
+        impersonate(AUDIT_TEST_USER);
+        verifyAuditQueries(true, getProjectName());
+        verifyAuditQueries(false, "Home");
         stopImpersonating();
+        permissionsHelper.removeUserRoleAssignment(AUDIT_TEST_USER, SEE_AUDIT_LOG_FOLDER_ROLE, getProjectName());
 
-        // now grant CanSeeAuditLog permission to our audit user and verify
-        // we see audit information
-        permissionsHelper.setSiteRoleUserPermissions(AUDIT_TEST_USER, "See Audit Log Events");
+        // Grant the "See Audit Log Events" root role to our audit user and verify we see audit information in this
+        // project and in /Home
+        permissionsHelper.setSiteRoleUserPermissions(AUDIT_TEST_USER, SEE_AUDIT_LOG_SITE_ROLE);
         impersonate(AUDIT_TEST_USER);
-        verifyAuditQueries(true);
+        verifyAuditQueries(true, getProjectName());
+        ExecuteQueryPage.beginAt(this, "Home", "auditLog", "SearchAuditEvent");
+        verifyAuditQueryEvent(this, "Query", SEARCH_TERM, 1);
 
         // cleanup
         stopImpersonating();
@@ -482,7 +500,7 @@ public void testDetailedQueryUpdateAuditLog() throws IOException, CommandExcepti
             //then create model (which has detailed audit log level)
             InsertRowsCommand insertCmd2 = new InsertRowsCommand("vehicle", "models");
             rowMap = new HashMap<>();
-            rowMap.put("manufacturerId", resp1.getRows().get(0).get("rowid"));
+            rowMap.put("manufacturerId", resp1.getRows().getFirst().get("rowid"));
             rowMap.put("name", "Soul");
             insertCmd2.addRow(rowMap);
             insertCmd2.execute(cn, AUDIT_DETAILED_TEST_PROJECT);
@@ -535,17 +553,17 @@ protected void verifyListAuditLogQueries(Visibility v)
         verifyAuditQueryEvent(this, "List", "Child List", 1, canSeeChild(v));
     }
 
-    protected void verifyAuditQueries(boolean canSeeAuditLog)
+    protected void verifyAuditQueries(boolean canSeeAuditLog, String containerPath)
     {
-        ExecuteQueryPage.beginAt(this, getProjectName(), "auditLog", "ContainerAuditEvent");
+        ExecuteQueryPage.beginAt(this, containerPath, "auditLog", "ContainerAuditEvent");
         if (canSeeAuditLog)
             verifyAuditQueryEvent(this, COMMENT_COLUMN, AUDIT_TEST_PROJECT + " was created", 1);
         else
             assertTextPresent("No data to show.");
 
-        ExecuteQueryPage.beginAt(this, getProjectName(), "auditLog", "GroupAuditEvent");
+        ExecuteQueryPage.beginAt(this, containerPath, "auditLog", "GroupAuditEvent");
         if (canSeeAuditLog)
-            verifyAuditQueryEvent(this, COMMENT_COLUMN, "The user " + AUDIT_TEST_USER + " was assigned to the security role Editor.", 1);
+            verifyAuditQueryEvent(this, COMMENT_COLUMN, "The user " + AUDIT_TEST_USER + " was assigned to the security role Editor.", 4);
         else
             assertTextPresent("No data to show.");
     }

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/tests/InlineImagesListTest.java

@@ -219,11 +219,7 @@ public final void testList() throws Exception
         // Mouse over the logo, migh help with the following mouse over the image.
         mouseOver(Locator.tagWithAttributeContaining("img", "src", "logo.image"));
         sleep(500);
-        mouseOver(Locator.xpath("//img[contains(@title, '" + LRG_PNG_FILE.getName() + "')]"));
-        longWait().until(ExpectedConditions.visibilityOfElementLocated(By.cssSelector("#helpDiv")));
-        String src = Locator.xpath("//div[@id='helpDiv']//img[contains(@src, 'download')]").findElement(getDriver()).getAttribute("src");
-        assertTrue("Wrong image in popup: " + src, src.contains(LRG_PNG_FILE.getName()));
-        assertEquals("Bad response from image pop-up", HttpStatus.SC_OK, WebTestHelper.getHttpResponse(src).getResponseCode());
+        verifyImagePopupInGrid(LRG_PNG_FILE);
 
         // Commenting out for now. There is a random behavior where sometimes the thumbnail image will not show up when you move from one cell to another.
         /*
@@ -303,7 +299,7 @@ public final void testList() throws Exception
         sleep(500);
         mouseOver(Locator.xpath("//img[contains(@title, '" + LRG_PNG_FILE.getName() + "')]"));
         shortWait().until(ExpectedConditions.visibilityOfElementLocated(By.cssSelector("#helpDiv")));
-        src = Locator.xpath("//div[@id='helpDiv']//img[contains(@src, 'download')]").findElement(getDriver()).getAttribute("src");
+        var src = Locator.xpath("//div[@id='helpDiv']//img[contains(@src, 'download')]").findElement(getDriver()).getAttribute("src");
         assertTrue("Wrong image in popup: " + src, src.contains(LRG_PNG_FILE.getName()));
         assertEquals("Bad response from image pop-up", HttpStatus.SC_OK, WebTestHelper.getHttpResponse(src).getResponseCode());
 

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

@@ -27,6 +27,7 @@
 import org.labkey.test.categories.Reports;
 import org.labkey.test.util.ApiPermissionsHelper;
 import org.labkey.test.util.DataRegionTable;
+import org.labkey.test.util.OptionalFeatureHelper;
 import org.labkey.test.util.RReportHelper;
 
 import java.util.Arrays;
@@ -50,6 +51,8 @@ public class ReportSharingTest extends BaseWebDriverTest
     @Override
     protected void doCleanup(boolean afterTest) throws TestTimeoutException
     {
+        OptionalFeatureHelper.resetOptionalFeature(createDefaultConnection(), "rReportCustomSharing");
+
         _containerHelper.deleteProject(getProjectName(),afterTest);
         _userHelper.deleteUsers(false, USER_DEV,USER_EDITOR,USER_NON_EDITOR);
     }
@@ -63,6 +66,8 @@ public static void setupProject()
 
     private void doSetup()
     {
+        OptionalFeatureHelper.setOptionalFeature(createDefaultConnection(), "rReportCustomSharing", true);
+
         _rReportHelper.ensureRConfig();
 
         _containerHelper.createProject(getProjectName(), null);