Generate RO bundle for containing path when requesting single file

Author: Mark Robinson

src/main/java/org/commonwl/viewer/cwl/CWLService.java

@@ -216,67 +216,6 @@ private void fillStepRunTypes(Workflow workflow, Map<String, JsonNode> packedFil
         }
     }
 
-    /**
-     * Find the main workflow object in the group of files being considered
-     * by finding the minimal inDegree in a graph of run: parameters within steps
-     * @return The file name/key of the workflow
-
-    private String findMainWorkflow() {
-        // Store the in degree of each workflow
-        Map<String, Integer> inDegrees = new HashMap<String, Integer>();
-        for (Map.Entry<String, JsonNode> doc : cwlDocs.entrySet()) {
-            if (doc.getValue().get(CLASS).asText().equals(WORKFLOW)) {
-                inDegrees.put(doc.getKey(), 0);
-            }
-        }
-
-        // Loop through documents and calculate in degrees
-        for (Map.Entry<String, JsonNode> doc : cwlDocs.entrySet()) {
-            JsonNode content = doc.getValue();
-            if (inDegrees.containsKey(doc.getKey())) {
-                // Parse workflow steps and see whether other workflows are run
-                JsonNode steps = content.get(STEPS);
-                if (steps.getClass() == ArrayNode.class) {
-                    // Explicit ID and other fields within each input list
-                    for (JsonNode step : steps) {
-                        String run = FilenameUtils.getName(extractRun(step));
-                        if (run != null && inDegrees.containsKey(run)) {
-                            inDegrees.put(run, inDegrees.get(run) + 1);
-                        }
-                    }
-                } else if (steps.getClass() == ObjectNode.class) {
-                    // ID is the key of each object
-                    Iterator<Map.Entry<String, JsonNode>> iterator = steps.fields();
-                    while (iterator.hasNext()) {
-                        Map.Entry<String, JsonNode> stepNode = iterator.next();
-                        JsonNode stepJson = stepNode.getValue();
-                        String run = FilenameUtils.getName(extractRun(stepJson));
-                        if (run != null && inDegrees.containsKey(run)) {
-                            inDegrees.put(run, inDegrees.get(run) + 1);
-                        }
-                    }
-                }
-            }
-        }
-
-        // Find a workflow with minimum inDegree and return
-        int minVal = Integer.MAX_VALUE;
-        String minKey = null;
-        for (Map.Entry<String, Integer> inDegree : inDegrees.entrySet()) {
-            if (inDegree.getValue() < minVal) {
-                minKey = inDegree.getKey();
-                minVal = inDegree.getValue();
-            }
-
-            // Early escape if minVal is already minimal
-            if (minVal == 0) {
-                return minKey;
-            }
-        }
-
-        return minKey;
-    }
-
     /**
      * Get the steps for a particular document
      * @param cwlDoc The document to get steps for

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

@@ -19,6 +19,7 @@
 
 package org.commonwl.viewer.researchobject;
 
+import org.apache.commons.io.FilenameUtils;
 import org.commonwl.viewer.github.GitHubService;
 import org.commonwl.viewer.github.GithubDetails;
 import org.commonwl.viewer.workflow.Workflow;
@@ -77,8 +78,12 @@ public void workflowROFromGithub(GitHubService githubService, GithubDetails gith
             throws IOException, InterruptedException {
         logger.info("Creating Research Object Bundle");
 
+        // Get the whole containing folder, not just the workflow itself
+        GithubDetails roDetails = new GithubDetails(githubInfo.getOwner(), githubInfo.getRepoName(),
+                githubInfo.getBranch(), FilenameUtils.getPath(githubInfo.getPath()));
+
         // Create a new Research Object Bundle with Github contents
-        ROBundle bundle = new ROBundle(githubService, githubInfo, commitSha,
+        ROBundle bundle = new ROBundle(githubService, roDetails, commitSha,
                 applicationName, applicationURL, singleFileSizeLimit);
 
         // Save the bundle to the storage location in properties

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

@@ -153,7 +153,8 @@ public ModelAndView getWorkflowByGithubDetails(@Value("${applicationURL}") Strin
             workflowFormValidator.validateAndParse(workflowForm, errors);
             if (errors.hasErrors()) {
                 redirectAttrs.addFlashAttribute("errors", errors);
-                return new ModelAndView("redirect:/");
+                return new ModelAndView("redirect:/?url=https://github.com/" +
+                        owner + "/" + repoName + "/tree/" + branch + "/" + path);
             } else {
                 workflowModel = workflowService.createWorkflow(githubDetails);
             }

src/main/java/org/commonwl/viewer/workflow/WorkflowFormValidator.java

@@ -75,7 +75,7 @@ public GithubDetails validateAndParse(WorkflowForm form, Errors e) {
                 }
             } else {
                 logger.error("The Github URL " + form.getGithubURL() + " is not valid");
-                e.rejectValue("githubURL", "githubURL.invalid");
+                e.rejectValue("githubURL", "githubURL.invalid", "You must enter a valid Github URL to a .cwl file");
             }
         } else {
             logger.error("Github URL is empty");

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

@@ -45,7 +45,7 @@ public class WorkflowService {
     private final GitHubService githubService;
     private final CWLService cwlService;
     private final WorkflowRepository workflowRepository;
-    private final org.commonwl.viewer.researchobject.ROBundleFactory ROBundleFactory;
+    private final ROBundleFactory ROBundleFactory;
     private final GraphVizService graphVizService;
     private final int cacheDays;