Remove directory viewing functionality

Author: MarkRobbo

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

@@ -28,7 +28,6 @@
 import org.commonwl.view.graphviz.GraphVizService;
 import org.commonwl.view.researchobject.ROBundleFactory;
 import org.commonwl.view.researchobject.ROBundleNotFoundException;
-import org.eclipse.egit.github.core.RepositoryContents;
 import org.eclipse.jgit.api.Git;
 import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.RefNotFoundException;
@@ -43,10 +42,8 @@
 import java.io.File;
 import java.io.IOException;
 import java.nio.file.Path;
-import java.util.ArrayList;
 import java.util.Calendar;
 import java.util.Date;
-import java.util.List;
 
 @Service
 public class WorkflowService {
@@ -118,30 +115,6 @@ public QueuedWorkflow getQueuedWorkflow(String id) {
         return queuedWorkflowRepository.findOne(id);
     }
 
-    /**
-     * Get a list of workflows from a directory in Github
-     * @param githubInfo Github information for the workflow
-     * @return The list of workflow names
-     */
-    public List<WorkflowOverview> getWorkflowsFromDirectory(GitDetails githubInfo) throws IOException {
-        List<WorkflowOverview> workflowsInDir = new ArrayList<>();
-        for (RepositoryContents content : githubService.getContents(githubInfo)) {
-            int eIndex = content.getName().lastIndexOf('.') + 1;
-            if (eIndex > 0) {
-                String extension = content.getName().substring(eIndex);
-                if (extension.equals("cwl")) {
-                    GitDetails githubFile = new GitDetails(githubInfo.getRepoUrl(),
-                            githubInfo.getBranch(), content.getPath(), githubInfo.getType());
-                    WorkflowOverview overview = cwlService.getWorkflowOverview(githubFile);
-                    if (overview != null) {
-                        workflowsInDir.add(overview);
-                    }
-                }
-            }
-        }
-        return workflowsInDir;
-    }
-
     /**
      * Get a queued workflow from the database
      * @param githubInfo Github information for the workflow
@@ -241,9 +214,10 @@ public File getROBundle(GitDetails gitDetails) throws ROBundleNotFoundException
      * @return A queued workflow model
      * @throws GitAPIException Git errors
      * @throws CWLValidationException cwltool errors
+     * @throws IOException Other file handling exceptions
      */
     public QueuedWorkflow createQueuedWorkflow(GitDetails gitInfo)
-            throws GitAPIException, CWLValidationException {
+            throws GitAPIException, CWLValidationException, IOException {
 
         QueuedWorkflow queuedWorkflow = new QueuedWorkflow();
 

src/main/resources/templates/selectworkflow.html

@@ -36,11 +36,6 @@
 import org.springframework.test.web.servlet.setup.MockMvcBuilders;
 import org.springframework.web.servlet.view.InternalResourceViewResolver;
 
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Arrays;
-
-import static org.hamcrest.Matchers.*;
 import static org.hamcrest.core.Is.is;
 import static org.mockito.Matchers.anyObject;
 import static org.mockito.Matchers.anyString;
@@ -203,73 +198,6 @@ public void directWorkflowURL() throws Exception {
 
     }
 
-    /**
-     * Displaying directories of workflows
-     */
-    @Test
-    public void directDirectoryURL() throws Exception {
-
-        // Workflow overviews for testing
-        WorkflowOverview overview1 = new WorkflowOverview("workflow1.cwl", "label1", "doc1");
-        WorkflowOverview overview2 = new WorkflowOverview("workflow2.cwl", "label2", "doc2");
-
-        // Mock service to return these overviews
-        WorkflowService mockWorkflowService = Mockito.mock(WorkflowService.class);
-        when(mockWorkflowService.getWorkflowsFromDirectory(anyObject()))
-                .thenReturn(new ArrayList<>())
-                .thenReturn(new ArrayList<>(Arrays.asList(overview1)))
-                .thenReturn(new ArrayList<>(Arrays.asList(overview1, overview2)))
-                .thenReturn(new ArrayList<>(Arrays.asList(overview1, overview2)))
-                .thenThrow(new IOException("Error getting contents"));
-
-        // Mock controller/MVC
-        WorkflowController workflowController = new WorkflowController(
-                Mockito.mock(WorkflowFormValidator.class),
-                mockWorkflowService,
-                Mockito.mock(GraphVizService.class));
-        MockMvc mockMvc = MockMvcBuilders
-                .standaloneSetup(workflowController)
-                .build();
-
-        // No workflows in directory, redirect with errors
-        mockMvc.perform(get("/workflows/github.com/owner/reponame/tree/branch/path/within"))
-                .andExpect(status().isFound())
-                .andExpect(flash().attributeExists("errors"))
-                .andExpect(redirectedUrl("/?url=https://github.com/owner/reponame/tree/branch/path/within"));
-
-        // 1 workflow in directory, redirect to it
-        mockMvc.perform(get("/workflows/github.com/common-workflow-language/workflows/tree/master/workflows/lobSTR"))
-                .andExpect(status().isFound())
-                .andExpect(redirectedUrl("/workflows/github.com/common-workflow-language/workflows/tree/master/workflows/lobSTR/workflow1.cwl"));
-
-        // Multiple workflows in directory, show list
-        mockMvc.perform(get("/workflows/github.com/common-workflow-language/workflows/tree/visu/workflows/scidap"))
-                .andExpect(status().isOk())
-                .andExpect(view().name("selectworkflow"))
-                .andExpect(model().attribute("githubDetails", allOf(
-                        hasProperty("owner", is("common-workflow-language")),
-                        hasProperty("repoName", is("workflows")),
-                        hasProperty("branch", is("visu")),
-                        hasProperty("path", is("workflows/scidap"))
-                )))
-                .andExpect(model().attribute("workflowOverviews",
-                        containsInAnyOrder(overview1, overview2)));
-
-        // Workflows at the base of a repository
-        mockMvc.perform(get("/workflows/github.com/genome/arvados_trial/tree/master"))
-                .andExpect(status().isOk())
-                .andExpect(view().name("selectworkflow"))
-                .andExpect(model().attribute("githubDetails",
-                        hasProperty("path", is("/"))));
-
-        // Error getting contents of Github directory, redirect with errors
-        mockMvc.perform(get("/workflows/github.com/owner/reponame/tree/branch/path/within"))
-                .andExpect(status().isFound())
-                .andExpect(flash().attributeExists("errors"))
-                .andExpect(redirectedUrl("/?url=https://github.com/owner/reponame/tree/branch/path/within"));
-
-    }
-
     /**
      * Endpoint for downloading RO bundle for a workflow
      */

src/test/java/org/commonwl/view/workflow/WorkflowControllerTest.java

@@ -25,22 +25,16 @@
 import org.commonwl.view.github.GitService;
 import org.commonwl.view.graphviz.GraphVizService;
 import org.commonwl.view.researchobject.ROBundleFactory;
-import org.eclipse.egit.github.core.RepositoryContents;
 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.Date;
 import java.util.HashMap;
-import java.util.List;
 
 import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
 import static org.mockito.Matchers.anyObject;
 import static org.mockito.Matchers.anyString;
 import static org.mockito.Mockito.when;
@@ -53,69 +47,6 @@ public class WorkflowServiceTest {
     @Rule
     public TemporaryFolder roBundleFolder = new TemporaryFolder();
 
-    /**
-     * Getting a list of workflow overviews from a directory
-     */
-    @Test
-    public void getWorkflowsFromDirectory() throws Exception {
-
-        // Mock Github service redirecting content query to the filesystem
-        GitService mockGithubService = Mockito.mock(GitService.class);
-        Answer contentsAnswer = new Answer<List<RepositoryContents>>() {
-            @Override
-            public List<RepositoryContents> answer(InvocationOnMock invocation) throws Throwable {
-                List<RepositoryContents> returnList = new ArrayList<>();
-
-                // Add all files from lobstr-v1 directory
-                File[] fileList = new File("src/test/resources/cwl/lobstr-v1/").listFiles();
-                for (File thisFile : fileList) {
-                    RepositoryContents contentsEntry = new RepositoryContents();
-                    if (thisFile.isFile()) {
-                        contentsEntry.setType(GitService.TYPE_FILE);
-                        contentsEntry.setSize(100);
-                        contentsEntry.setName(thisFile.getName());
-                        contentsEntry.setPath("workflows/lobSTR/" + thisFile.getName());
-                        returnList.add(contentsEntry);
-                    }
-                }
-
-                return returnList;
-            }
-        };
-        when(mockGithubService.getContents(anyObject())).thenAnswer(contentsAnswer);
-
-        // Mock CWL service which returns simple overview once simulating 1 workflow found
-        CWLService mockCWLService = Mockito.mock(CWLService.class);
-        when(mockCWLService.getWorkflowOverview(anyObject()))
-                .thenReturn(new WorkflowOverview("workflow.cwl", "label", "doc"))
-                .thenReturn(new WorkflowOverview("workflow2.cwl", "label2", "doc2"))
-                .thenReturn(null);
-
-        // Create service under test
-        WorkflowService testWorkflowService = new WorkflowService(
-                mockGithubService, mockCWLService,
-                Mockito.mock(WorkflowRepository.class),
-                Mockito.mock(QueuedWorkflowRepository.class),
-                Mockito.mock(ROBundleFactory.class),
-                Mockito.mock(GraphVizService.class),
-                Mockito.mock(CWLToolRunner.class), 1);
-
-        // Get a list of workflows from the directory
-        List<WorkflowOverview> list = testWorkflowService.getWorkflowsFromDirectory(
-                Mockito.mock(GitDetails.class));
-
-        // 1 workflow should be found
-        assertTrue(list.size() == 2);
-        assertEquals("workflow.cwl", list.get(0).getFileName());
-        assertEquals("label", list.get(0).getLabel());
-        assertEquals("doc", list.get(0).getDoc());
-
-        assertEquals("workflow2.cwl", list.get(1).getFileName());
-        assertEquals("label2", list.get(1).getLabel());
-        assertEquals("doc2", list.get(1).getDoc());
-
-    }
-
     /**
      * Getting a workflow when cache has expired
      * And a new workflow needs to be created