Add unit tests for FileUtilsTest

Author: kinow

pom.xml

@@ -174,10 +174,11 @@
       <version>1.17.3</version>
       <scope>test</scope>
     </dependency>
+    <!-- We use mockito-inline as it supports mocking static methods -->
     <dependency>
       <groupId>org.mockito</groupId>
-      <artifactId>mockito-all</artifactId>
-      <version>1.10.19</version>
+      <artifactId>mockito-inline</artifactId>
+      <version>4.7.0</version>
       <scope>test</scope>
     </dependency>
   </dependencies>

src/main/java/org/commonwl/view/Scheduler.java

@@ -115,34 +115,23 @@ public void clearTmpDir() {
      * @param temporaryDirectory temporary directory
      */
     private void clearDirectory(String temporaryDirectory) {
-        final Path dir = Paths.get(temporaryDirectory);
         final Instant cutoff = Instant.now().minus(Duration.ofDays(TMP_DIR_AGE_LIMIT_DAYS));
-        // TODO: Commons IO 2.12 has a constructor that takes an Instant; drop the Date#from call here when we upgrade.
-        final AgeFileFilter fileAndDirFilter = new AgeFileFilter(Date.from(cutoff));
-        final AccumulatorPathVisitor visitor = AccumulatorPathVisitor.withLongCounters(fileAndDirFilter, fileAndDirFilter);
-
-        // Walk the files.
-        try {
-            Files.walkFileTree(dir, Collections.emptySet(), /* maxDepth */ 1, visitor);
-        } catch (IOException e) {
-            // Really unexpected. walkFileTree should throw an IllegalArgumentException for negative maxDepth (clearly
-            // not happening here), a SecurityException if the security manager denies access, or this IOException in
-            // the cases where an I/O error happened (disk error, OS error, file not found, etc.). So just a warning.
-            logger.warn(String.format("Unexpected I/O error was thrown walking directory [%s]: %s", dir, e.getMessage()), e);
-        }
 
-        // Delete the directories accumulated by the visitor.
-        final List<Path> dirList = visitor.getDirList();
-        dirList.forEach(tooOldDeleteMe -> {
-            File fileToDelete = tooOldDeleteMe.toFile();
-            try {
-                FileUtils.forceDelete(fileToDelete);
-            } catch (IOException e) {
-                // Here we probably have a more serious case. Since the Git repository, RO directory, or graphs are
-                // not expected to be in use, and the application must have access, I/O errors are not expected and
-                // must be treated as errors.
-                logger.error(String.format("Failed to delete old temporary file or directory [%s]: %s", fileToDelete.getAbsolutePath(), e.getMessage()), e);
+        File temporaryDirectoryFile = new File(temporaryDirectory);
+        String[] files = temporaryDirectoryFile.list(new AgeFileFilter(Date.from(cutoff)));
+
+        if (files != null && files.length > 0) {
+            for (String fileName : files) {
+                File fileToDelete = new File(temporaryDirectoryFile, fileName);
+                try {
+                    FileUtils.forceDelete(fileToDelete);
+                } catch (IOException e) {
+                    // Here we probably have a more serious case. Since the Git repository, RO directory, or graphs are
+                    // not expected to be in use, and the application must have access, I/O errors are not expected and
+                    // must be treated as errors.
+                    logger.error(String.format("Failed to delete old temporary file or directory [%s]: %s", fileToDelete.getAbsolutePath(), e.getMessage()), e);
+                }
             }
-        });
+        }
     }
 }

src/main/java/org/commonwl/view/researchobject/ROBundleFactory.java

@@ -19,11 +19,11 @@
 
 package org.commonwl.view.researchobject;
 
-import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.FilenameUtils;
 import org.apache.taverna.robundle.Bundle;
 import org.apache.taverna.robundle.fs.BundleFileSystem;
 import org.commonwl.view.git.GitDetails;
+import org.commonwl.view.util.FileUtils;
 import org.commonwl.view.workflow.Workflow;
 import org.commonwl.view.workflow.WorkflowRepository;
 import org.slf4j.Logger;
@@ -81,25 +81,10 @@ public void createWorkflowRO(Workflow workflow)
 
         // Save the bundle to the storage location in properties
         Path bundleLocation = roBundleService.saveToFile(bundle);
-        // The RoBundleService#saveToFile call above will delegate to Taverna's
-        // Bundles.closeAndSaveBundle, which empties the bundle temporary
-        // directory without deleting the directory itself. The following call is
-        // just for cleaning it up.
-        if (bundle != null) {
-            try {
-                BundleFileSystem fs = (BundleFileSystem) bundle.getFileSystem();
-                File tmpDir = new File(System.getProperty("java.io.tmpdir"));
-                // The file system source will be something like /tmp/bundles_dir/hash/bundle.zip,
-                // and we want /tmp/hash to be deleted. N.B. Taverna uses the temporary directory
-                // for the temporary bundles' directory, not the bundles file specified by Spring.
-                String bundleTmpDirName = fs.getSource().toAbsolutePath().getParent().getFileName().toString();
-                File bundleTmpDir = new File(tmpDir, bundleTmpDirName);
-                if (bundleTmpDir.exists() && bundleTmpDir.isDirectory()) {
-                    FileUtils.forceDelete(bundleTmpDir);
-                }
-            } catch (IOException e) {
-                logger.warn(String.format("Failed to delete temporary directory for bundle [%s]: %s", bundle.getSource(), e.getMessage()), e);
-            }
+        try {
+            FileUtils.deleteBundleTemporaryDirectory(bundle);
+        } catch (IOException e) {
+            logger.warn(String.format("Failed to delete temporary directory for bundle [%s]: %s", bundle.getSource(), e.getMessage()), e);
         }
 
         // Add RO Bundle to associated workflow model