Delete git repository and bundle directories on any errors

src/main/java/org/commonwl/view/cwl/CWLToolRunner.java

@@ -24,6 +24,7 @@
 import org.commonwl.view.git.GitSemaphore;
 import org.commonwl.view.git.GitService;
 import org.commonwl.view.researchobject.ROBundleFactory;
+import org.commonwl.view.util.FileUtils;
 import org.commonwl.view.workflow.QueuedWorkflow;
 import org.commonwl.view.workflow.QueuedWorkflowRepository;
 import org.commonwl.view.workflow.Workflow;
@@ -78,9 +79,10 @@ public void createWorkflowFromQueued(QueuedWorkflow queuedWorkflow)
         GitDetails gitInfo = tempWorkflow.getRetrievedFrom();
         final String repoUrl = gitInfo.getRepoUrl();
         // Parse using cwltool and replace in database
+        Git repo = null;
         try {
             boolean safeToAccess = gitSemaphore.acquire(repoUrl);
-            Git repo = gitService.getRepository(gitInfo, safeToAccess);
+            repo = gitService.getRepository(gitInfo, safeToAccess);
             Path localPath = repo.getRepository().getWorkTree().toPath();
             Path workflowFile = localPath.resolve(gitInfo.getPath()).normalize().toAbsolutePath();
             Workflow newWorkflow = cwlService.parseWorkflowWithCwltool(
@@ -106,16 +108,19 @@ public void createWorkflowFromQueued(QueuedWorkflow queuedWorkflow)
             logger.error("Jena query exception ", ex);
             queuedWorkflow.setCwltoolStatus(CWLToolStatus.ERROR);
             queuedWorkflow.setMessage("An error occurred when executing a query on the SPARQL store");
+            FileUtils.deleteGitRepository(repo);
         } catch (CWLValidationException ex) {
             logger.error(ex.getMessage(), ex);
             queuedWorkflow.setCwltoolStatus(CWLToolStatus.ERROR);
             queuedWorkflow.setMessage(ex.getMessage());
+            FileUtils.deleteGitRepository(repo);
         } catch (Exception ex) {
             logger.error("Unexpected error", ex);
             queuedWorkflow.setCwltoolStatus(CWLToolStatus.ERROR);
             queuedWorkflow.setMessage("Whoops! Cwltool ran successfully, but an unexpected " +
                     "error occurred in CWLViewer!\n" +
                     "Help us by reporting it on Gitter or a Github issue\n");
+            FileUtils.deleteGitRepository(repo);
         } finally {
             gitSemaphore.release(repoUrl);
             queuedWorkflowRepository.save(queuedWorkflow);

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

@@ -128,6 +128,7 @@ public Bundle createBundle(Workflow workflow, GitDetails gitInfo) throws IOExcep
         Bundle bundle = Bundles.createBundle();
         Manifest manifest = bundle.getManifest();
 
+        Path bundlePath = null;
         // Simplified attribution for RO bundle
         try {
             manifest.setId(new URI(workflow.getPermalink()));
@@ -143,18 +144,23 @@ public Bundle createBundle(Workflow workflow, GitDetails gitInfo) throws IOExcep
 
             // Make a directory in the RO bundle to store the files
             Path bundleRoot = bundle.getRoot();
-            Path bundlePath = bundleRoot.resolve("workflow");
+            bundlePath = bundleRoot.resolve("workflow");
             Files.createDirectory(bundlePath);
 
             // Add the files from the repo to this workflow
             Set<HashableAgent> authors = new HashSet<>();
 
             boolean safeToAccess = gitSemaphore.acquire(gitInfo.getRepoUrl());
+            Git gitRepo = null;
             try {
-                Git gitRepo = gitService.getRepository(workflow.getRetrievedFrom(), safeToAccess);
+                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);
+            } catch (GitAPIException | IOException e) {
+                org.commonwl.view.util.FileUtils.deleteGitRepository(gitRepo);
+                FileUtils.forceDelete(bundlePath.toFile());
+                throw e;
             } finally {
                 gitSemaphore.release(gitInfo.getRepoUrl());
             }
@@ -217,6 +223,7 @@ 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);
+            FileUtils.forceDelete(bundlePath.toFile());
         }
 
         // Return the completed bundle

src/main/java/org/commonwl/view/util/FileUtils.java

@@ -0,0 +1,22 @@
+package org.commonwl.view.util;
+
+import org.eclipse.jgit.api.Git;
+
+import java.io.IOException;
+
+/**
+ * File utilities for CWL Viewer.
+ *
+ * <p>Uses other utilities, such as Apache Commons IO's {@code FileUtils}, but
+ * with refinements specific for CWL Viewer (e.g. handling Git repositories).</p>
+ */
+public class FileUtils {
+
+    private FileUtils() {}
+
+    public static void deleteGitRepository(Git repo) throws IOException {
+        if (repo != null && repo.getRepository() != null && repo.getRepository().getDirectory().exists()) {
+            org.apache.commons.io.FileUtils.forceDelete(repo.getRepository().getDirectory());
+        }
+    }
+}

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

@@ -19,18 +19,6 @@
 
 package org.commonwl.view.workflow;
 
-import java.io.File;
-import java.io.IOException;
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.nio.file.Paths;
-import java.util.ArrayList;
-import java.util.Calendar;
-import java.util.Date;
-import java.util.List;
-import java.util.Objects;
-import java.util.Optional;
-
 import org.commonwl.view.cwl.CWLService;
 import org.commonwl.view.cwl.CWLToolRunner;
 import org.commonwl.view.cwl.CWLToolStatus;
@@ -40,6 +28,7 @@
 import org.commonwl.view.graphviz.GraphVizService;
 import org.commonwl.view.researchobject.ROBundleFactory;
 import org.commonwl.view.researchobject.ROBundleNotFoundException;
+import org.commonwl.view.util.FileUtils;
 import org.eclipse.jgit.api.Git;
 import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.RefNotFoundException;
@@ -52,6 +41,18 @@
 import org.springframework.data.domain.Pageable;
 import org.springframework.stereotype.Service;
 
+import java.io.File;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.ArrayList;
+import java.util.Calendar;
+import java.util.Date;
+import java.util.List;
+import java.util.Objects;
+import java.util.Optional;
+
 @Service
 public class WorkflowService {
 
@@ -295,9 +296,9 @@ public QueuedWorkflow createQueuedWorkflow(GitDetails gitInfo)
             throws GitAPIException, WorkflowNotFoundException, IOException {
         QueuedWorkflow queuedWorkflow;
 
+        Git repo = null;
         try {
             boolean safeToAccess = gitSemaphore.acquire(gitInfo.getRepoUrl());
-            Git repo = null;
             while (repo == null) {
                 try {
                     repo = gitService.getRepository(gitInfo, safeToAccess);
@@ -366,6 +367,10 @@ public QueuedWorkflow createQueuedWorkflow(GitDetails gitInfo)
                 logger.error("Could not update workflow with cwltool", e);
             }
 
+        } catch (GitAPIException | RuntimeException | IOException e) {
+            logger.warn(String.format("Failed to create Queued Workflow: %s - Temporary files will be deleted", e.getMessage()), e);
+            FileUtils.deleteGitRepository(repo);
+            throw e;
         } finally {
             gitSemaphore.release(gitInfo.getRepoUrl());
         }