Testing construction of Research Object Bundles

Only uses a single level of files currently

Author: Mark Robinson

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

@@ -237,4 +237,11 @@ public Path saveToFile(Path directory) throws IOException {
         return bundleLocation;
     }
 
+    /**
+     * Getter method for the bundle
+     * @return The RO bundle
+     */
+    public Bundle getBundle() {
+        return bundle;
+    }
 }

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

@@ -0,0 +1,139 @@
+package org.commonwl.view.researchobject;
+
+import org.apache.commons.io.FileUtils;
+import org.apache.taverna.robundle.Bundle;
+import org.apache.taverna.robundle.Bundles;
+import org.apache.taverna.robundle.manifest.Manifest;
+import org.commonwl.view.github.GitHubService;
+import org.commonwl.view.github.GithubDetails;
+import org.eclipse.egit.github.core.*;
+import org.junit.Rule;
+import org.junit.Test;
+import org.junit.rules.TemporaryFolder;
+import org.mockito.Mockito;
+import org.mockito.invocation.InvocationOnMock;
+import org.mockito.stubbing.Answer;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.List;
+
+import static org.junit.Assert.*;
+import static org.mockito.Matchers.anyObject;
+import static org.mockito.Mockito.when;
+
+public class ROBundleTest {
+
+    /**
+     * Use a temporary directory for testing
+     */
+    @Rule
+    public TemporaryFolder roBundleFolder = new TemporaryFolder();
+
+    /**
+     * Generate a Research Object bundle from lobstr-v1 and check it
+     */
+    @Test
+    public void generateAndSaveROBundle() throws Exception {
+
+        // Get mock Github service
+        GitHubService mockGithubService = getMock();
+
+        // Create new RO bundle
+        GithubDetails lobSTRv1Details = new GithubDetails("common-workflow-language", "workflows",
+                "933bf2a1a1cce32d88f88f136275535da9df0954", "workflows/lobSTR");
+        ROBundle bundle = new ROBundle(mockGithubService, lobSTRv1Details, "CWL Viewer",
+                "https://view.commonwl.org", 5242880);
+
+        // Check bundle exists
+        assertNotNull(bundle.getBundle());
+
+        // Check basic manifest metadata
+        Manifest manifest = bundle.getBundle().getManifest();
+        assertEquals("CWL Viewer", manifest.getCreatedBy().getName());
+        assertEquals("https://view.commonwl.org", manifest.getCreatedBy().getUri().toString());
+        assertEquals("Mark Robinson", manifest.getAuthoredBy().get(0).getName());
+        assertEquals(10, manifest.getAggregates().size());
+
+        // Save and check it exists in the temporary folder
+        bundle.saveToFile(roBundleFolder.getRoot().toPath());
+        File[] fileList =  roBundleFolder.getRoot().listFiles();
+        assertTrue(fileList.length == 1);
+        for (File ro : fileList) {
+            assertTrue(ro.getName().endsWith(".zip"));
+            Bundle savedBundle = Bundles.openBundle(ro.toPath());
+            assertNotNull(savedBundle);
+        }
+
+    }
+
+    /**
+     * Get a mock Github service redirecting file downloads to file system
+     * and providing translation from the file system to Github API returns
+     * @return The constructed mock object
+     */
+    private GitHubService getMock() throws Exception {
+
+        GitHubService mockGithubService = Mockito.mock(GitHubService.class);
+        Answer fileAnswer = new Answer<String>() {
+            @Override
+            public String answer(InvocationOnMock invocation) throws Throwable {
+                Object[] args = invocation.getArguments();
+                GithubDetails details = (GithubDetails) args[0];
+                File workflowFile = new File("src/test/resources/cwl/lobstr-v1/"
+                        + details.getPath().replace("workflows/lobSTR/", ""));
+                return FileUtils.readFileToString(workflowFile);
+            }
+        };
+        when(mockGithubService.downloadFile(anyObject())).thenAnswer(fileAnswer);
+        when(mockGithubService.downloadFile(anyObject(), anyObject())).thenAnswer(fileAnswer);
+
+        Answer contentsAnswer = new Answer<List<RepositoryContents>>() {
+            @Override
+            public List<RepositoryContents> answer(InvocationOnMock invocation) throws Throwable {
+                File[] fileList = new File("src/test/resources/cwl/lobstr-v1/").listFiles();
+
+                // Add all files from lobstr-v1 directory
+                List<RepositoryContents> returnList = new ArrayList<>();
+                for (File thisFile : fileList) {
+                    if (thisFile.isFile()) {
+                        RepositoryContents singleFile = new RepositoryContents();
+                        singleFile.setType(GitHubService.TYPE_FILE);
+                        singleFile.setName(thisFile.getName());
+                        singleFile.setPath("workflows/lobSTR/" + thisFile.getName());
+                        returnList.add(singleFile);
+                    }
+                }
+
+                return returnList;
+            }
+        };
+        when(mockGithubService.getContents(anyObject())).thenAnswer(contentsAnswer);
+
+        Answer commitsAnswer = new Answer<List<RepositoryCommit>>() {
+            @Override
+            public List<RepositoryCommit> answer(InvocationOnMock invocation) throws Throwable {
+                Object[] args = invocation.getArguments();
+                GithubDetails details = (GithubDetails) args[0];
+
+                // Make up a commit for the file and return it
+                List<RepositoryCommit> commitList = new ArrayList<>();
+                RepositoryCommit commit = new RepositoryCommit();
+
+                User author = new User();
+                author.setName("Mark Robinson");
+                author.setHtmlUrl("https://github.com/MarkRobbo");
+                commit.setAuthor(author);
+                commit.setSha("933bf2a1a1cce32d88f88f136275535da9df0954");
+                commit.setCommit(new Commit().setAuthor(new CommitUser().setName("Mark Robinson")));
+                commitList.add(commit);
+
+                return commitList;
+            }
+        };
+        when(mockGithubService.getCommits(anyObject())).thenAnswer(commitsAnswer);
+
+        return mockGithubService;
+    }
+
+}