Delete git repository directory after RO Bundle is (re)created, success or not.

Author: kinow

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

@@ -73,16 +73,16 @@ public class ROBundleService {
     private final Logger logger = LoggerFactory.getLogger(this.getClass());
 
     // Services
-    private GraphVizService graphVizService;
-    private GitService gitService;
-    private RDFService rdfService;
-    private CWLTool cwlTool;
-    private GitSemaphore gitSemaphore;
+    private final GraphVizService graphVizService;
+    private final GitService gitService;
+    private final RDFService rdfService;
+    private final CWLTool cwlTool;
+    private final GitSemaphore gitSemaphore;
 
     // Configuration variables
-    private Agent appAgent;
-    private int singleFileSizeLimit;
-    private Path bundleStorage;
+    private final Agent appAgent;
+    private final int singleFileSizeLimit;
+    private final Path bundleStorage;
 
     // Pattern for extracting version from a cwl file
     private final String CWL_VERSION_REGEX = "cwlVersion:\\s*\"?(?:cwl:)?([^\\s\"]+)\"?";
@@ -129,6 +129,7 @@ public Bundle createBundle(Workflow workflow, GitDetails gitInfo) throws IOExcep
         Manifest manifest = bundle.getManifest();
 
         // Simplified attribution for RO bundle
+        Git gitRepo = null;
         try {
             manifest.setId(new URI(workflow.getPermalink()));
 
@@ -150,7 +151,8 @@ public Bundle createBundle(Workflow workflow, GitDetails gitInfo) throws IOExcep
             Set<HashableAgent> authors = new HashSet<>();
 
             boolean safeToAccess = gitSemaphore.acquire(gitInfo.getRepoUrl());
-            try (Git gitRepo = gitService.getRepository(workflow.getRetrievedFrom(), safeToAccess)) {
+            try {
+                gitRepo = gitService.getRepository(workflow.getRetrievedFrom(), safeToAccess);
                 Path relativePath = Paths.get(FilenameUtils.getPath(gitInfo.getPath()));
                 Path gitPath = gitRepo.getRepository().getWorkTree().toPath().resolve(relativePath);
                 addFilesToBundle(gitInfo, bundle, bundlePath, gitRepo, gitPath, authors, workflow);
@@ -194,7 +196,7 @@ public Bundle createBundle(Workflow workflow, GitDetails gitInfo) throws IOExcep
                 addAggregation(bundle, manifestAnnotations,
                         "merged.cwl", cwlTool.getPackedVersion(rawUrl));
             } catch (CWLValidationException ex) {
-                logger.error("Could not pack workflow when creating Research Object", ex.getMessage());
+                logger.error("Could not pack workflow when creating Research Object", ex);
             }
             String rdfUrl = workflow.getIdentifier();
             if (rdfService.graphExists(rdfUrl)) {
@@ -216,6 +218,19 @@ public Bundle createBundle(Workflow workflow, GitDetails gitInfo) throws IOExcep
             logger.error("Error creating URI for RO Bundle", ex);
         } catch (GitAPIException ex) {
             logger.error("Error getting repository to create RO Bundle", ex);
+        } finally {
+            if (gitRepo != null) {
+                gitRepo.close();
+                File repoDir = gitRepo.getRepository().getDirectory();
+                try {
+                    FileUtils.deleteDirectory(repoDir.getParentFile());
+                } catch (IOException e) {
+                    logger.warn(
+                            String.format("Failed to delete Git repository directory: %s", repoDir.getAbsolutePath()),
+                            e
+                    );
+                }
+            }
         }
 
         // Return the completed bundle

src/main/java/org/commonwl/view/workflow/WorkflowService.java

@@ -456,18 +456,11 @@ public Workflow findByCommitAndPath(String commitID, String path, Optional<Strin
     public PathResource getWorkflowGraph(String format, GitDetails gitDetails)
             throws WorkflowNotFoundException, IOException {
         // Determine file extension from format
-        String extension;
-        switch (format) {
-            case "svg":
-            case "png":
-                extension = format;
-                break;
-            case "xdot":
-                extension = "dot";
-                break;
-            default:
-                throw new WorkflowNotFoundException();
-        }
+        String extension = switch (format) {
+            case "svg", "png" -> format;
+            case "xdot" -> "dot";
+            default -> throw new WorkflowNotFoundException();
+        };
 
         // Get workflow
         Workflow workflow = getWorkflow(gitDetails);