[bot] Fast-forward for 25.9.0

src/org/labkey/remoteapi/issues/IssueModel.java

@@ -1,6 +1,7 @@
 package org.labkey.remoteapi.issues;
 
 import org.json.JSONObject;
+import org.json.JSONParserConfiguration;
 import org.labkey.api.collections.CaseInsensitiveHashMap;
 
 import java.io.File;
@@ -27,7 +28,8 @@ public IssueModel setProperties(Map<String, String> properties)
 
     public JSONObject toJSON()
     {
-        var json = new JSONObject(_properties);
+        // Ensure that null values are sent instead of omitted
+        var json = new JSONObject(_properties, new JSONParserConfiguration().withUseNativeNulls(true));
 
         // handle attachments
         if (!_attachments.isEmpty())

src/org/labkey/test/AssayAPITest.java

@@ -311,8 +311,8 @@ public void testImportRun_dataRows() throws Exception
         assayHelper.importAssay(assayId, runName, dataRowsInvalidResultFileDirectory, getProjectName(), Collections.singletonMap("RunFileField", CREST_FILE.getName()), Collections.emptyMap(), "DataFileField: Invalid file path: ../");
 
         // valid run file and valid result file
-        FileBrowserHelper.FileDetailInfo runFileInfo = _fileBrowserHelper.getFileDetailInfo(getProjectName(), CREST_FILE.getName());
-        FileBrowserHelper.FileDetailInfo resultFileInfo = _fileBrowserHelper.getFileDetailInfo(getProjectName(), SCREENSHOT_FILE.getName());
+        FileBrowserHelper.FileDetailInfo runFileInfo = FileBrowserHelper.getFileDetailInfo(getProjectName(), CREST_FILE.getName());
+        FileBrowserHelper.FileDetailInfo resultFileInfo = FileBrowserHelper.getFileDetailInfo(getProjectName(), SCREENSHOT_FILE.getName());
         List<Pair<String, String>> scenarios = List.of(new Pair<>(CREST_FILE.getName(), SCREENSHOT_FILE.getName()),
                 new Pair<>(runFileInfo.absoluteFilePath(), resultFileInfo.absoluteFilePath()),
                 new Pair<>(runFileInfo.webDavUrl(), resultFileInfo.webDavUrl()),
@@ -388,7 +388,7 @@ public void testGpatSaveBatch() throws Exception
         goToModule("FileContent");
         _fileBrowserHelper.uploadFile(HELP_ICON_FILE);
         goToManageAssays();
-        FileBrowserHelper.FileDetailInfo runFileInfo = _fileBrowserHelper.getFileDetailInfo(getProjectName(), "help.jpg");
+        FileBrowserHelper.FileDetailInfo runFileInfo = FileBrowserHelper.getFileDetailInfo(getProjectName(), "help.jpg");
         ((APIAssayHelper) _assayHelper).saveBatch(assayName, "Valid absolute path", Collections.singletonMap("RunFileField", runFileInfo.absoluteFilePath()), resultRows, getProjectName(), null);
         ((APIAssayHelper) _assayHelper).saveBatch(assayName, "Valid webdav full path", Collections.singletonMap("RunFileField", runFileInfo.webDavUrl()), resultRows, getProjectName(), null);
         ((APIAssayHelper) _assayHelper).saveBatch(assayName, "Valid webdav relative path", Collections.singletonMap("RunFileField", runFileInfo.webDavUrlRelative()), resultRows, getProjectName(), null);

src/org/labkey/test/Locator.java

@@ -19,6 +19,7 @@
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.mutable.MutableObject;
 import org.intellij.lang.annotations.Language;
+import org.jetbrains.annotations.Contract;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
 import org.labkey.test.selenium.LazyWebElement;
@@ -373,11 +374,13 @@ protected static <T> T extractInputFromFluentWait(FluentWait<T> wait)
         return wrappedContext.getValue();
     }
 
+    @Contract(pure = true)
     public LazyWebElement<?> findWhenNeeded(SearchContext context)
     {
         return new LazyWebElement<>(this, context);
     }
 
+    @Contract(pure = true)
     public RefindingWebElement refindWhenNeeded(SearchContext context)
     {
         return new RefindingWebElement(this, context);
@@ -391,11 +394,13 @@ public WebElement findElement(SearchContext context)
                 new NoSuchElementException("Unable to find element: " + getFindDescription(context)));
     }
 
+    @Contract(pure = true)
     public WebElement findElementOrNull(SearchContext context)
     {
         return findOptionalElement(context).orElse(null);
     }
 
+    @Contract(pure = true)
     public Optional<WebElement> findOptionalElement(SearchContext context)
     {
         List<WebElement> elements = findElements(context);
@@ -404,6 +409,7 @@ public Optional<WebElement> findOptionalElement(SearchContext context)
         return Optional.of(elements.get(0));
     }
 
+    @Contract(pure = true)
     @Override
     public List<WebElement> findElements(SearchContext context)
     {
@@ -454,11 +460,13 @@ public List<WebElement> findElements(SearchContext context)
         }
     }
 
+    @Contract(pure = true)
     public boolean existsIn(SearchContext context)
     {
         return findElementOrNull(context) != null;
     }
 
+    @Contract(pure = true)
     public boolean isDisplayed(SearchContext context)
     {
         WebElement element = findElementOrNull(context);
@@ -471,6 +479,7 @@ public boolean isDisplayed(SearchContext context)
      * @param context Search context.
      * @return True if there are any elements visible, false otherwise.
      */
+    @Contract(pure = true)
     public boolean areAnyVisible(SearchContext context)
     {
         List<WebElement> elements = findElements(context);

src/org/labkey/test/TestFileUtils.java

@@ -19,6 +19,7 @@
 import org.apache.commons.compress.archivers.ArchiveStreamFactory;
 import org.apache.commons.compress.archivers.tar.TarArchiveEntry;
 import org.apache.commons.compress.archivers.tar.TarArchiveInputStream;
+import org.apache.commons.io.FileSystem;
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.StringUtils;
@@ -27,8 +28,6 @@
 import org.apache.pdfbox.Loader;
 import org.apache.pdfbox.pdmodel.PDDocument;
 import org.apache.pdfbox.text.PDFTextStripper;
-import org.apache.poi.xssf.streaming.SXSSFRow;
-import org.apache.poi.xssf.streaming.SXSSFWorkbook;
 import org.bouncycastle.jce.provider.BouncyCastleProvider;
 import org.bouncycastle.openpgp.PGPCompressedData;
 import org.bouncycastle.openpgp.PGPEncryptedDataList;
@@ -41,12 +40,10 @@
 import org.bouncycastle.openpgp.operator.jcajce.JcePBEDataDecryptorFactoryBuilder;
 import org.bouncycastle.util.io.Streams;
 import org.jetbrains.annotations.NotNull;
-import org.labkey.serverapi.reader.Readers;
 import org.openqa.selenium.NotFoundException;
 
 import java.io.BufferedInputStream;
 import java.io.BufferedOutputStream;
-import java.io.BufferedReader;
 import java.io.ByteArrayInputStream;
 import java.io.File;
 import java.io.FileInputStream;
@@ -71,6 +68,7 @@
 import java.util.List;
 import java.util.Set;
 import java.util.TreeSet;
+import java.util.regex.Pattern;
 import java.util.stream.Collectors;
 import java.util.zip.GZIPInputStream;
 import java.util.zip.ZipEntry;
@@ -707,34 +705,15 @@ public static byte[] decrypt(byte[] encrypted, char[] passPhrase) throws IOExcep
         return Streams.readAll(ld.getInputStream());
     }
 
+    private static final Pattern badChars = Pattern.compile("[\\\\:/\\[\\]?*|]");
 
-    public static File convertTabularToXlsx(File tabularFile, String delimiter, String sheetName, String xlsxFileName) throws IOException, PGPException
+    /**
+     * Determining expected file names for downloaded files that are named according to some
+     * value that might include characters that are not legal for files
+     * @see FileSystem#toLegalFileName(String, char)
+     */
+    public static String makeLegalFileName(String candidate)
     {
-        File excelFile = new File(getTestTempDir(), xlsxFileName);
-        FileUtils.forceMkdirParent(excelFile);
-
-        try(SXSSFWorkbook workBook = new SXSSFWorkbook(1000); // holds 1000 rows at a time
-            BufferedReader br = Readers.getReader(tabularFile);
-            FileOutputStream out =  new FileOutputStream(excelFile))
-        {
-            var sheet = workBook.createSheet(sheetName);
-
-            String currentLine;
-            int rowNum=0;
-
-            while ((currentLine = br.readLine()) != null)
-            {
-                String str[] = currentLine.split(delimiter);
-                SXSSFRow currentRow = sheet.createRow(rowNum);
-                for (int i = 0; i < str.length; i++)
-                {
-                    currentRow.createCell(i).setCellValue(str[i]);
-                }
-                rowNum++;
-            }
-            workBook.write(out);    // flush remaining rows
-        }
-
-        return excelFile;
+        return badChars.matcher(candidate).replaceAll("_");
     }
 }

src/org/labkey/test/TestProperties.java

@@ -257,6 +257,11 @@ public static boolean isTrialServer()
         return getBooleanProperty("webtest.server.trial", false);
     }
 
+    public static boolean isRemoteNameValidationEnabled()
+    {
+        return getBooleanProperty("webtest.remote.domain.validation", false);
+    }
+
     public static boolean isCheckerFatal()
     {
         return "true".equals(System.getProperty("webtest.checker.fatal"));

src/org/labkey/test/WebDriverWrapper.java

@@ -2129,6 +2129,14 @@ public long doAndMaybeWaitForPageToLoad(int msWait, Supplier<Boolean> action)
         return loadTimer.elapsed().toMillis();
     }
 
+    public void doAndWaitForNewWindow(Runnable action)
+    {
+        Set<String> windows = getDriver().getWindowHandles();
+        action.run();
+        switchToWindow(windows.size());
+        waitForDocument();
+    }
+
     public long doAndWaitForWindow(Runnable action, String windowName)
     {
         String initialWindow = getDriver().getWindowHandle();

src/org/labkey/test/components/bootstrap/Panel.java

@@ -71,26 +71,20 @@ public class ElementCache extends Component<?>.ElementCache
         protected final WebElement panelBody = Locator.byClass("panel-body").findWhenNeeded(this);
     }
 
-    public static class PanelFinder extends WebDriverComponentFinder<Panel<?>, PanelFinder>
+    protected static abstract class AbstractPanelFinder<C extends Panel<?>, F extends AbstractPanelFinder<C, F>> extends WebDriverComponentFinder<C, F>
     {
-        private final Locator.XPathLocator _baseLocator = Locator.tagWithClass("div", "panel-default");
+        private final Locator.XPathLocator _baseLocator = Locator.tagWithClass("div", "panel");
         private String _title = null;
 
-        public PanelFinder(WebDriver driver)
+        public AbstractPanelFinder(WebDriver driver)
         {
             super(driver);
         }
 
-        public PanelFinder withTitle(String title)
+        public F withTitle(String title)
         {
             _title = title;
-            return this;
-        }
-
-        @Override
-        protected Panel<?> construct(WebElement el, WebDriver driver)
-        {
-            return new PanelImpl(el, driver);
+            return getThis();
         }
 
         @Override
@@ -103,6 +97,26 @@ protected Locator locator()
                 return _baseLocator;
         }
     }
+
+    public static class PanelFinder extends AbstractPanelFinder<Panel<?>, PanelFinder>
+    {
+        public PanelFinder(WebDriver driver)
+        {
+            super(driver);
+        }
+
+        @Override
+        protected PanelFinder getThis()
+        {
+            return this;
+        }
+
+        @Override
+        protected Panel<?> construct(WebElement el, WebDriver driver)
+        {
+            return new PanelImpl(el, driver);
+        }
+    }
 }
 
 class PanelImpl extends Panel<ElementCache>