Merge pull request #97 from common-workflow-language/footer-change

Change to footer to update year and correct typo

Author: MarkRobbo

src/main/java/org/commonwl/view/MongoConfig.java

@@ -17,7 +17,7 @@
  * under the License.
  */
 
-package org.commonwl.viewer;
+package org.commonwl.view;
 
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.annotation.Bean;

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

@@ -27,7 +27,6 @@
 import org.apache.taverna.robundle.manifest.Manifest;
 import org.apache.taverna.robundle.manifest.PathMetadata;
 import org.apache.taverna.robundle.manifest.Proxy;
-import org.commonwl.viewer.services.GitHubService;
 import org.commonwl.view.github.GitHubService;
 import org.commonwl.view.github.GithubDetails;
 import org.eclipse.egit.github.core.CommitUser;
@@ -137,19 +136,6 @@ public Bundle newBundleFromGithub(GithubDetails githubInfo) throws IOException {
 
     }
 
-    /**
-     * Save the Research Object bundle to disk
-     * @param roBundle The bundle to be saved
-     * @return The path to the research object
-     * @throws IOException Any errors in saving
-     */
-    public Path saveToFile(Bundle roBundle) throws IOException {
-        String fileName = "bundle-" + java.util.UUID.randomUUID() + ".zip";
-        Path bundleLocation = Files.createFile(bundleStorage.resolve(fileName));
-        Bundles.closeAndSaveBundle(roBundle, bundleLocation);
-        return bundleLocation;
-    }
-
     /**
      * Add files to this bundle from a list of Github repository contents
      * @param bundle The RO bundle to add files/directories to
@@ -207,13 +193,12 @@ private void addFilesToBundle(Bundle bundle, GithubDetails githubInfo,
                         fileContent = githubService.downloadFile(githubFile, commitSha);
 
                         // Save file to research object bundle
-                        Path bundleFilePath = path.resolve(repoContent.getName());
                         Bundles.setStringValue(bundleFilePath, fileContent);
 
                         // Set retrieved information for this file in the manifest
                         aggregation = bundle.getManifest().getAggregation(bundleFilePath);
                         aggregation.setRetrievedFrom(rawURI);
-                        aggregation.setRetrievedBy(thisApp);
+                        aggregation.setRetrievedBy(appAgent);
                         aggregation.setRetrievedOn(aggregation.getCreatedOn());
                     } else {
                         logger.info("File " + repoContent.getName() + " is too large to download - " +
@@ -279,14 +264,14 @@ private void addFilesToBundle(Bundle bundle, GithubDetails githubInfo,
 
     /**
      * Save the Research Object bundle to disk
-     * @param directory The directory in which the RO will be saved
+     * @param roBundle The bundle to be saved
      * @return The path to the research object
      * @throws IOException Any errors in saving
      */
-    public Path saveToFile(Path directory) throws IOException {
+    public Path saveToFile(Bundle roBundle) throws IOException {
         String fileName = "bundle-" + java.util.UUID.randomUUID() + ".zip";
-        Path bundleLocation = Files.createFile(directory.resolve(fileName));
-        Bundles.closeAndSaveBundle(bundle, bundleLocation);
+        Path bundleLocation = Files.createFile(bundleStorage.resolve(fileName));
+        Bundles.closeAndSaveBundle(roBundle, bundleLocation);
         return bundleLocation;
     }
 

src/main/resources/templates/fragments/footer.html

@@ -29,7 +29,7 @@
             <hr />
             <div class="col-lg-12 muted text-center">
                 <a href="https://github.com/common-workflow-language/cwlviewer" rel="noopener" target="_blank">CWL Viewer</a>
-                &copy; 2016 <a href="https://github.com/common-workflow-language/" rel="noopener" target="_blank">Common Workflow Project</a>
+                &copy; 2016-2017 <a href="https://github.com/common-workflow-language/" rel="noopener" target="_blank">Common Workflow Language Project</a>
                 and <a href="https://github.com/orgs/common-workflow-language/people" rel="noopener" target="_blank">contributors</a>,
                 distributed under <a href="https://www.apache.org/licenses/LICENSE-2.0" rel="noopener" target="_blank">Apache license, version 2.0</a>
                 <br />

src/test/java/org/commonwl/view/researchobject/ROBundleServiceTest.java

@@ -35,6 +35,7 @@
 import org.mockito.stubbing.Answer;
 
 import java.io.File;
+import java.net.URI;
 import java.nio.file.Path;
 import java.util.ArrayList;
 import java.util.List;
@@ -119,9 +120,12 @@ public void filesOverLimit() throws Exception {
         Manifest manifest = bundle.getManifest();
 
         // Check files are externally linked in the aggregate
-        Path bundleRoot = bundle.getRoot().resolve("workflow");
+        assertEquals(12, manifest.getAggregates().size());
+
         PathMetadata urlAggregate = manifest.getAggregation(
-                bundleRoot.resolve("lobSTR-demo.url"));
+                new URI("https://raw.githubusercontent.com/common-workflow-language/workflows/" +
+                        "933bf2a1a1cce32d88f88f136275535da9df0954/workflows/lobSTR/models/" +
+                        "illumina_v3.pcrfree.stepmodel"));
         assertEquals("Mark Robinson", urlAggregate.getAuthoredBy().get(0).getName());
 
     }