Merge remote-tracking branch 'origin/develop' into fb_mail_transport_via_graph

labkey-bpatel · labkey-bpatel · commit c98b8ec90581 · 2026-03-04T13:43:10.000-08:00
diff --git a/gradle.properties b/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
 
diff --git a/src/org/labkey/test/WebDriverWrapper.java b/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)
diff --git a/src/org/labkey/test/components/domain/DomainFieldRow.java b/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);
     }
 
diff --git a/src/org/labkey/test/components/ui/grids/ResponsiveGrid.java b/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) ||
diff --git a/src/org/labkey/test/tests/AuditLogTest.java b/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 +65,11 @@
 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;
 
 @Category({Daily.class, Hosting.class})
 @BaseWebDriverTest.ClassTimeout(minutes = 9)
@@ -79,21 +80,18 @@ 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 +375,37 @@ 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, "org.labkey.api.security.roles.CanSeeAuditLogFolderRole", PermissionsHelper.MemberType.user, getProjectName());
+        impersonate(AUDIT_TEST_USER);
+        verifyAuditQueries(true, getProjectName());
+        verifyAuditQueries(false, "Home");
         stopImpersonating();
+        permissionsHelper.removeUserRoleAssignment(AUDIT_TEST_USER, "org.labkey.api.security.roles.CanSeeAuditLogFolderRole", 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, "org.labkey.api.security.roles.CanSeeAuditLogRole");
         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 +498,7 @@ 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 +551,17 @@ 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.");
     }
diff --git a/src/org/labkey/test/tests/GpatAssayTest.java b/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;
     }
 
diff --git a/src/org/labkey/test/util/TestDataGenerator.java b/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()
diff --git a/src/org/labkey/test/util/data/TestDataUtils.java b/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();
         }
     }
 
diff --git a/src/org/labkey/test/util/selenium/JavascriptExecutorWrapper.java b/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);
+    }
+}
diff --git a/src/org/labkey/test/util/selenium/WebDriverUtils.java b/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}).
diff --git a/src/org/labkey/test/util/selenium/WebElementUtils.java b/src/org/labkey/test/util/selenium/WebElementUtils.java

Original file line number	Diff line number	Diff line change
`@@ -769,6 +769,8 @@ public DomainFieldRow clickRemoveOntologyConcept()`
`769`	`769`
`770`	`770`	`public void setAllowMultipleSelections(Boolean allowMultipleSelections)`
`771`	`771`	`{`
	`772`	`+ WebDriverWrapper.waitFor(() -> elementCache().allowMultipleSelectionsCheckbox.isDisplayed(),`
	`773`	`+ "Allow Multiple Selections checkbox did not become visible", 2000);`
`772`	`774`	`elementCache().allowMultipleSelectionsCheckbox.set(allowMultipleSelections);`
`773`	`775`	`}`
`774`	`776`
Original file line number	Diff line number	Diff line change
`@@ -75,7 +75,7 @@ public WebElement getComponentElement()`
`75`	`75`
`76`	`76`	`public Boolean isLoaded()`
`77`	`77`	`{`
`78`		`- return getComponentElement().isDisplayed() &&`
	`78`	`+ return WebElementUtils.checkVisibility(getComponentElement()) &&`
`79`	`79`	`!Locators.loadingGrid.existsIn(this) &&`
`80`	`80`	`!Locators.spinner.existsIn(this) &&`
`81`	`81`	`(Locator.tag("td").existsIn(this) \|\|`
Original file line number	Diff line number	Diff line change
`@@ -581,14 +581,13 @@ public static List<List<String>> readRowsFromFile(File file, CSVFormat format) t`
`581`	`581`	`public static List<String> parseMultiValueText(String multiValueString) throws IOException`
`582`	`582`	`{`
`583`	`583`	`CSVFormat format = CSVFormat.RFC4180.builder()`
`584`		`- .setIgnoreSurroundingSpaces(true).get();`
	`584`	`+ .setIgnoreSurroundingSpaces(true).setTrim(true).get();`
`585`	`585`	`try (CSVParser parser = format.parse(new StringReader(multiValueString)))`
`586`	`586`	`{`
`587`	`587`	`List<CSVRecord> records = parser.getRecords();`
`588`		`- List<List<String>> list = records.stream().map(CSVRecord::toList).toList();`
`589`		`- if (list.size() != 1)`
	`588`	`+ if (records.size() != 1)`
`590`	`589`	`throw new IllegalArgumentException("Invalid multi-value text string: " + multiValueString);`
`591`		`- return list.getFirst();`
	`590`	`+ return records.getFirst().toList();`
`592`	`591`	`}`
`593`	`592`	`}`
`594`	`593`