Ensure asynchronous cwltool is on same git checkout

... by aquiring its own semaphore within the async job and getting
the git repository again.

Note that this will mean an uncessary duplicate "fetch" - however
this also mean that the async "retryCwltool" works as intended
by pulling the branch again.

Author: stain

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

@@ -19,23 +19,27 @@
 
 package org.commonwl.view.cwl;
 
+import java.io.IOException;
+import java.nio.file.Path;
+import java.util.Date;
+
 import org.apache.jena.query.QueryException;
+import org.commonwl.view.git.GitDetails;
+import org.commonwl.view.git.GitSemaphore;
+import org.commonwl.view.git.GitService;
 import org.commonwl.view.researchobject.ROBundleFactory;
 import org.commonwl.view.workflow.QueuedWorkflow;
 import org.commonwl.view.workflow.QueuedWorkflowRepository;
 import org.commonwl.view.workflow.Workflow;
 import org.commonwl.view.workflow.WorkflowRepository;
+import org.eclipse.jgit.api.Git;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.scheduling.annotation.Async;
 import org.springframework.scheduling.annotation.EnableAsync;
 import org.springframework.stereotype.Component;
 
-import java.io.File;
-import java.io.IOException;
-import java.util.Date;
-
 /**
  * Replace existing workflow with the one given by cwltool
  */
@@ -50,31 +54,38 @@ public class CWLToolRunner {
     private final CWLService cwlService;
     private final ROBundleFactory roBundleFactory;
     private final String cwlToolVersion;
+    private final GitSemaphore gitSemaphore;
+    private final GitService gitService;
 
     @Autowired
-    public CWLToolRunner(WorkflowRepository workflowRepository,
-                         QueuedWorkflowRepository queuedWorkflowRepository,
-                         CWLService cwlService,
-                         CWLTool cwlTool,
-                         ROBundleFactory roBundleFactory) {
+    public CWLToolRunner(WorkflowRepository workflowRepository, QueuedWorkflowRepository queuedWorkflowRepository,
+            CWLService cwlService, CWLTool cwlTool, ROBundleFactory roBundleFactory, GitSemaphore gitSemaphore,
+            GitService gitService) {
         this.workflowRepository = workflowRepository;
         this.queuedWorkflowRepository = queuedWorkflowRepository;
         this.cwlService = cwlService;
         this.cwlToolVersion = cwlTool.getVersion();
         this.roBundleFactory = roBundleFactory;
+        this.gitSemaphore = gitSemaphore;
+        this.gitService = gitService;
     }
 
     @Async
-    public void createWorkflowFromQueued(QueuedWorkflow queuedWorkflow, File workflowFile)
+    public void createWorkflowFromQueued(QueuedWorkflow queuedWorkflow)
             throws IOException, InterruptedException {
 
         Workflow tempWorkflow = queuedWorkflow.getTempRepresentation();
-
+        GitDetails gitInfo = tempWorkflow.getRetrievedFrom();
+        final String repoUrl = gitInfo.getRepoUrl();
         // Parse using cwltool and replace in database
         try {
+            boolean safeToAccess = gitSemaphore.acquire(repoUrl);
+            Git repo = gitService.getRepository(gitInfo, safeToAccess);
+            Path localPath = repo.getRepository().getWorkTree().toPath();
+            Path workflowFile = localPath.resolve(gitInfo.getPath()).normalize().toAbsolutePath();
             Workflow newWorkflow = cwlService.parseWorkflowWithCwltool(
                     tempWorkflow,
-                    workflowFile);
+                    workflowFile.toFile());
 
             // Success
             newWorkflow.setRetrievedFrom(tempWorkflow.getRetrievedFrom());
@@ -105,6 +116,7 @@ public void createWorkflowFromQueued(QueuedWorkflow queuedWorkflow, File workflo
                     "error occurred in CWLViewer!\n" +
                     "Help us by reporting it on Gitter or a Github issue\n");
         } finally {
+            gitSemaphore.release(repoUrl);
             queuedWorkflowRepository.save(queuedWorkflow);
         }
 

src/main/java/org/commonwl/view/git/GitService.java

@@ -19,6 +19,16 @@
 
 package org.commonwl.view.git;
 
+import static org.apache.jena.ext.com.google.common.io.Files.createTempDir;
+
+import java.io.IOException;
+import java.net.URI;
+import java.net.URISyntaxException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.HashSet;
+import java.util.Set;
+
 import org.apache.commons.codec.digest.DigestUtils;
 import org.commonwl.view.researchobject.HashableAgent;
 import org.eclipse.jgit.api.Git;
@@ -33,16 +43,6 @@
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.stereotype.Service;
 
-import java.io.IOException;
-import java.net.URI;
-import java.net.URISyntaxException;
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.util.HashSet;
-import java.util.Set;
-
-import static org.apache.jena.ext.com.google.common.io.Files.createTempDir;
-
 /**
  * Handles Git related functionality
  */
@@ -82,7 +82,6 @@ public Git getRepository(GitDetails gitDetails, boolean reuseDir)
                     // Check if folder already exists
                     Path repoDir = gitStorage.resolve(baseName);
                     if (Files.isReadable(repoDir) && Files.isDirectory(repoDir)) {
-                        repo = Git.open(repoDir.toFile());
                         repo.fetch().call();
                     } else {
                         // Create a folder and clone repository into it

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

@@ -19,6 +19,16 @@
 
 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 org.commonwl.view.cwl.CWLService;
 import org.commonwl.view.cwl.CWLToolRunner;
 import org.commonwl.view.cwl.CWLToolStatus;
@@ -38,16 +48,6 @@
 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;
-
 @Service
 public class WorkflowService {
 
@@ -320,7 +320,7 @@ public QueuedWorkflow createQueuedWorkflow(GitDetails gitInfo)
             // ASYNC OPERATIONS
             // Parse with cwltool and update model
             try {
-                cwlToolRunner.createWorkflowFromQueued(queuedWorkflow, workflowFile);
+                cwlToolRunner.createWorkflowFromQueued(queuedWorkflow);
             } catch (Exception e) {
                 logger.error("Could not update workflow with cwltool", e);
             }
@@ -341,17 +341,10 @@ public void retryCwltool(QueuedWorkflow queuedWorkflow) {
         queuedWorkflow.setMessage(null);
         queuedWorkflow.setCwltoolStatus(CWLToolStatus.RUNNING);
         queuedWorkflowRepository.save(queuedWorkflow);
-        GitDetails gitDetails = queuedWorkflow.getTempRepresentation().getRetrievedFrom();
-        boolean safeToAccess = gitSemaphore.acquire(gitDetails.getRepoUrl());
         try {
-            Git repo = gitService.getRepository(gitDetails, safeToAccess);
-            File localPath = repo.getRepository().getWorkTree();
-            Path pathToWorkflowFile = localPath.toPath().resolve(gitDetails.getPath()).normalize().toAbsolutePath();
-            cwlToolRunner.createWorkflowFromQueued(queuedWorkflow, new File(pathToWorkflowFile.toString()));
+            cwlToolRunner.createWorkflowFromQueued(queuedWorkflow);
         } catch (Exception e) {
             logger.error("Could not update workflow with cwltool", e);
-        } finally {
-            gitSemaphore.release(gitDetails.getRepoUrl());
         }
     }