From bf0556d339c46650a7b39c37a0546fb440875bf0 Mon Sep 17 00:00:00 2001
From: Mark Robinson <mark@goldtek.co.uk>
Date: Tue, 22 Aug 2017 12:00:27 +0100
Subject: [PATCH] Update lobstr example branch

---
 .../org/commonwl/view/git/GitService.java     | 21 ++++++++++---------
 src/main/resources/templates/index.html       |  2 +-
 2 files changed, 12 insertions(+), 11 deletions(-)

diff --git a/src/main/java/org/commonwl/view/git/GitService.java b/src/main/java/org/commonwl/view/git/GitService.java
index 12ea6d78..510cdf71 100644
--- a/src/main/java/org/commonwl/view/git/GitService.java
+++ b/src/main/java/org/commonwl/view/git/GitService.java
@@ -19,16 +19,6 @@
 
 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;
@@ -43,6 +33,16 @@
 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
  */
@@ -82,6 +82,7 @@ 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
diff --git a/src/main/resources/templates/index.html b/src/main/resources/templates/index.html
index 5d0d5aba..35ba3c16 100644
--- a/src/main/resources/templates/index.html
+++ b/src/main/resources/templates/index.html
@@ -53,7 +53,7 @@ <h2>Workflow URL</h2>
                         <strong>Don't know what to view?</strong> Try these from <i>common-workflow-language/workflows</i>:
                         <a class="example" href="https://github.com/common-workflow-language/workflows/tree/master/workflows/compile/compile1.cwl">compile</a>,
                         <a class="example" href="https://github.com/common-workflow-language/workflows/tree/master/workflows/make-to-cwl/dna.cwl">make-to-cwl</a>,
-                        <a class="example" href="https://github.com/common-workflow-language/workflows/tree/master/workflows/lobSTR/lobSTR-workflow.cwl">lobSTR</a>
+                        <a class="example" href="https://github.com/common-workflow-language/workflows/tree/lobstr-v1/workflows/lobSTR/lobSTR-workflow.cwl">lobSTR</a>
                         or <a href="/workflows">explore the collection</a>
                     </div>
                     <form id="add" action="#" th:action="@{/workflows}" th:object="${workflowForm}" method="POST">