Remove redundant mentions of Github

Author: MarkRobbo

src/main/java/org/commonwl/view/cwl/CWLToolRunner.java

@@ -85,7 +85,7 @@ public void createWorkflowFromQueued(QueuedWorkflow queuedWorkflow, File workflo
             workflowRepository.save(newWorkflow);
 
             // Generate RO bundle
-            roBundleFactory.workflowROFromGithub(newWorkflow);
+            roBundleFactory.createWorkflowRO(newWorkflow);
 
             // Mark success on queue
             queuedWorkflow.setCwltoolStatus(CWLToolStatus.SUCCESS);

src/main/java/org/commonwl/view/cwl/CWLToolStatus.java

@@ -4,5 +4,8 @@
  * Cwltool run status
  */
 public enum CWLToolStatus {
-    RUNNING, ERROR, SUCCESS
+    DOWNLOADING,
+    RUNNING,
+    ERROR,
+    SUCCESS
 }

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

@@ -63,7 +63,7 @@ public ROBundleFactory(ROBundleService roBundleService,
      * @throws IOException Any API errors which may have occurred
      */
     @Async
-    public void workflowROFromGithub(Workflow workflow)
+    public void createWorkflowRO(Workflow workflow)
             throws IOException, InterruptedException {
         logger.info("Creating Research Object Bundle");
 
@@ -72,7 +72,7 @@ public void workflowROFromGithub(Workflow workflow)
         GitDetails roDetails = new GitDetails(githubInfo.getRepoUrl(), githubInfo.getBranch(),
                 FilenameUtils.getPath(githubInfo.getPath()));
 
-        // Create a new Research Object Bundle with Github contents
+        // Create a new Research Object Bundle
         Bundle bundle = roBundleService.createBundle(workflow, roDetails);
 
         // Save the bundle to the storage location in properties

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

@@ -129,7 +129,7 @@ public Bundle createBundle(Workflow workflow, GitDetails gitInfo) throws IOExcep
             Path bundlePath = bundleRoot.resolve("workflow");
             Files.createDirectory(bundlePath);
 
-            // Add the files from the Github repo to this workflow
+            // Add the files from the repo to this workflow
             Set<HashableAgent> authors = new HashSet<>();
             Git gitRepo = gitService.getRepository(workflow.getRetrievedFrom());
             Path relativePath = Paths.get(FilenameUtils.getPath(gitInfo.getPath()));
@@ -199,7 +199,7 @@ public Bundle createBundle(Workflow workflow, GitDetails gitInfo) throws IOExcep
     }
 
     /**
-     * Add files to this bundle from a list of Github repository contents
+     * Add files to this bundle from a list of repository contents
      * @param gitDetails The Git information for the repository
      * @param bundle The RO bundle to add files/directories to
      * @param bundlePath The current path within the RO bundle

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

@@ -106,7 +106,7 @@ public String searchWorkflows(Model model,
      * @return The workflow view with new workflow as a model
      */
     @PostMapping("/workflows")
-    public ModelAndView newWorkflowFromGithubURL(@Valid WorkflowForm workflowForm, BindingResult bindingResult) {
+    public ModelAndView createWorkflow(@Valid WorkflowForm workflowForm, BindingResult bindingResult) {
 
         // Run validator which checks the git URL is valid
         GitDetails gitInfo = workflowFormValidator.validateAndParse(workflowForm, bindingResult);
@@ -122,7 +122,7 @@ public ModelAndView newWorkflowFromGithubURL(@Valid WorkflowForm workflowForm, B
                     workflow = workflowService.createQueuedWorkflow(gitInfo).getTempRepresentation();
                 } catch (GitAPIException ex) {
                     bindingResult.rejectValue("url", "git.retrievalError");
-                    logger.error("Github API Error", ex);
+                    logger.error("Git API Error", ex);
                     return new ModelAndView("index");
                 } catch (WorkflowNotFoundException ex) {
                     bindingResult.rejectValue("url", "git.pathTraversal");
@@ -363,10 +363,10 @@ public FileSystemResource getTempGraphAsPng(@PathVariable("queueID") String queu
 
 
     /**
-     * Extract the Github path from the end of a full request string
+     * Extract the path from the end of a full request string
      * @param path The full request string path
      * @param startSlashNum The ordinal slash index of the start of the path
-     * @return THe Github path from the end
+     * @return The path from the end
      */
     public static String extractPath(String path, int startSlashNum) {
         int pathStartIndex = StringUtils.ordinalIndexOf(path, "/", startSlashNum);
@@ -452,7 +452,7 @@ private ModelAndView getWorkflow(GitDetails gitDetails, RedirectAttributes redir
                         queued = workflowService.createQueuedWorkflow(gitDetails);
                     } catch (GitAPIException ex) {
                         errors.rejectValue("url", "git.retrievalError", "The workflow could not be retrieved from the Git repository using the details given");
-                        logger.error("Github API Error", ex);
+                        logger.error("Git API Error", ex);
                     } catch (WorkflowNotFoundException ex) {
                         errors.rejectValue("url", "git.pathTraversal", "The path given did not resolve to a location within the repository");
                     } catch (IOException ex) {

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

@@ -86,7 +86,7 @@ public Page<Workflow> searchWorkflowsJson(Model model,
     }
 
     /**
-     * Create a new workflow from the given github URL
+     * Create a new workflow from the given URL
      * @param url The URL of the workflow
      * @return Appropriate response code and optional JSON string with message
      */
@@ -139,7 +139,7 @@ public ResponseEntity<?> newWorkflowFromGithubURLJson(@RequestParam(value="url")
     }
 
     /**
-     * Get the JSON representation of a workflow from Github details
+     * Get the JSON representation of a workflow from Github or Gitlab details
      * @param domain The domain of the hosting site, Github or Gitlab
      * @param owner The owner of the Github repository
      * @param repoName The name of the repository

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

@@ -292,7 +292,7 @@ public void retryCwltool(QueuedWorkflow queuedWorkflow) {
      */
     private void generateROBundle(Workflow workflow) {
         try {
-            ROBundleFactory.workflowROFromGithub(workflow);
+            ROBundleFactory.createWorkflowRO(workflow);
         } catch (Exception ex) {
             logger.error("Error creating RO Bundle", ex);
         }

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

@@ -63,7 +63,7 @@ public void bundleForValidWorkflow() throws Exception {
         ROBundleFactory factory = new ROBundleFactory(mockROBundleService, mockRepository);
 
         // Attempt to add RO to workflow
-        factory.workflowROFromGithub(validWorkflow);
+        factory.createWorkflowRO(validWorkflow);
 
         assertEquals("test/path/to/check/for.zip", validWorkflow.getRoBundlePath());