Merge remote-tracking branch 'origin/master' into 1.2.1-RC1

Author: MarkRobbo

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());
         }
     }