Add TestFileUtils.deleteDirWithRetry method.

src/org/labkey/test/TestFileUtils.java

@@ -21,6 +21,7 @@
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.StringUtils;
+import org.apache.commons.lang3.SystemUtils;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.apache.pdfbox.Loader;
@@ -40,6 +41,7 @@
 import org.jetbrains.annotations.NotNull;
 import org.labkey.api.util.FileUtil;
 import org.jetbrains.annotations.Nullable;
+import org.labkey.api.util.StringUtilsLabKey;
 import org.openqa.selenium.NotFoundException;
 
 import java.io.BufferedInputStream;
@@ -57,6 +59,7 @@
 import java.io.Writer;
 import java.nio.charset.Charset;
 import java.nio.charset.StandardCharsets;
+import java.nio.file.AccessDeniedException;
 import java.nio.file.FileVisitResult;
 import java.nio.file.Files;
 import java.nio.file.Path;
@@ -71,10 +74,13 @@
 import java.util.Set;
 import java.util.TreeSet;
 import java.util.stream.Collectors;
+import java.util.stream.Stream;
 import java.util.zip.GZIPInputStream;
 import java.util.zip.ZipEntry;
 import java.util.zip.ZipInputStream;
 
+import static org.labkey.api.util.DebugInfoDumper.dumpHeap;
+import static org.labkey.test.WebDriverWrapper.sleep;
 import static org.labkey.test.util.TestDataGenerator.CHARSET_STRING;
 import static org.labkey.test.util.TestDataGenerator.randomInt;
 import static org.labkey.test.util.TestDataGenerator.randomName;
@@ -445,6 +451,81 @@ public static void deleteDir(File dir)
         }
     }
 
+    /**
+     * Deletes a directory and all its contents, retrying up to 10 times with a 10-second delay between attempts.
+     * <p>
+     * Before each attempt, the directory and all its children are marked writable to handle read-only files or
+     * directories. This is primarily intended to work around Windows file-locking issues where an external process
+     * may hold a lock on the directory or its contents.
+     * <p>
+     * On the final failed attempt, a heap dump is captured for diagnostics. On Windows, the list of running
+     * processes is also logged to help identify what may be holding the lock.
+     *
+     * @param dir the directory to delete
+     * @throws AccessDeniedException if access is denied on all 10 attempts
+     * @throws IOException if an I/O error occurs on all 10 attempts
+     * @throws Exception if an unexpected error occurs
+     */
+    public static void deleteDirWithRetry(File dir) throws Exception
+    {
+        // Sometimes on Windows the directory could be locked, maybe by an external process, or the child directory is
+        // readonly. Use a retry mechanism to set the writeable flag and then try to delete the parent directory.
+        for (int attempt = 1; attempt <= 10; attempt++) {
+            try
+            {
+                dir.setWritable(true, false);
+
+                // Wrap in a try to close the stream.
+                try (Stream<Path> files = Files.walk(dir.toPath())) {
+                    files.forEach(p -> p.toFile().setWritable(true, false));
+                }
+
+                FileUtils.deleteDirectory(dir);
+                LOG.info(String.format("Deletion of directory %s was successful.", dir));
+                break;
+            } catch (AccessDeniedException deniedException) {
+                // Yes I know AccessDeniedException is a subset of an IOException, but I wanted to log explicitly a
+                // failure and retry because of an AccessDeniedException from some other IOException.
+                LOG.warn(String.format("Access denied trying to delete directory %s. Error: %s. Waiting 10s and retrying. Attempt %d of 10.",
+                        dir, deniedException.getMessage(), attempt));
+                if (attempt == 10) throw deniedException;
+                sleep(10_000);
+            }
+            catch (IOException ioException) {
+                LOG.warn(String.format("IOException trying to delete directory %s. Error: %s. Waiting 10s and retrying. Attempt %d of 10.",
+                        dir, ioException.getMessage(), attempt));
+                if (attempt == 10)
+                {
+                    LOG.info("Dump the heap.");
+                    dumpHeap();
+
+                    if (SystemUtils.IS_OS_WINDOWS) {
+                        try {
+                            LOG.info("Lock diagnostic...");
+                            ProcessBuilder pb = new ProcessBuilder("tasklist");
+                            pb.redirectErrorStream(true);
+                            Process p = pb.start();
+                            try {
+                                String output = new String(p.getInputStream().readAllBytes(), StringUtilsLabKey.DEFAULT_CHARSET);
+                                LOG.info("Running processes:\n" + output);
+                            }
+                            finally
+                            {
+                                // Don't leak the process resource.
+                                p.destroy();
+                            }
+                        } catch (IOException diagnosticException) {
+                            LOG.warn("Failed to run lock diagnostic: " + diagnosticException.getMessage());
+                        }
+                    }
+                    throw ioException;
+                }
+                sleep(10_000);
+            }
+        }
+
+    }
+
     private static void checkFileLocation(File file)
     {
         try

src/org/labkey/test/tests/assay/AssayTransformMissingParentDirTest.java

@@ -1,6 +1,5 @@
 package org.labkey.test.tests.assay;
 
-import org.apache.commons.io.FileUtils;
 import org.junit.Test;
 import org.junit.experimental.categories.Category;
 import org.labkey.api.util.FileUtil;
@@ -15,8 +14,6 @@
 import org.labkey.test.params.assay.GeneralAssayDesign;
 
 import java.io.File;
-import java.io.IOException;
-import java.nio.file.AccessDeniedException;
 import java.nio.file.Files;
 import java.nio.file.Path;
 
@@ -48,29 +45,8 @@ public void testMissingParentDirectoryRegression() throws Exception
         assayDesignerPage.addTransformScript(transformFile);
         assayDesignerPage.clickSave();
 
-        // Now delete the parent dir to ensure we handle it reasonably. On Windows something locks the directory, maybe
-        // an external process. If that happens sleep for a second and try again.
-        for (int attempt = 1; attempt <= 10; attempt++) {
-            try
-            {
-                FileUtils.deleteDirectory(parentDir.toFile());
-                log(String.format("Deletion of directory %s was successful.", parentDir));
-                break;
-            } catch (AccessDeniedException deniedException) {
-                // Yes I know AccessDeniedException is a subset of an IOException, but I wanted to log explicitly a
-                // failure and retry because of an AccessDeniedException from some other IOException.
-                log(String.format("Access denied trying to delete directory %s. Error: %s. Waiting 10s and retrying. Attempt %d of 10.",
-                        parentDir, deniedException.getMessage(), attempt));
-                if (attempt == 10) throw deniedException;
-                sleep(10_000);
-            }
-            catch (IOException ioException) {
-                log(String.format("IOException trying to delete directory %s. Error: %s. Waiting 10s and retrying. Attempt %d of 10.",
-                        parentDir, ioException.getMessage(), attempt));
-                if (attempt == 10) throw ioException;
-                sleep(10_000);
-            }
-        }
+        // Now delete the parent dir to ensure we handle it reasonably
+        TestFileUtils.deleteDirWithRetry(parentDir.toFile());
 
         // Attempt to import data and verify a reasonable error message is shown
         String importData = """