Improve error handling

Author: MarkRobbo

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

@@ -39,6 +39,7 @@
 import org.commonwl.view.graphviz.ModelDotWriter;
 import org.commonwl.view.graphviz.RDFDotWriter;
 import org.commonwl.view.workflow.Workflow;
+import org.commonwl.view.workflow.WorkflowNotFoundException;
 import org.commonwl.view.workflow.WorkflowOverview;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -169,19 +170,30 @@ public Workflow parseWorkflowNative(File workflowFile, String packedWorkflowId)
             // Parse file as yaml
             JsonNode cwlFile = yamlStringToJson(readFileToString(workflowFile));
 
+            // Check packed workflow occurs
             if (packedWorkflowId != null) {
-                for (JsonNode jsonNode : cwlFile.get(DOC_GRAPH)) {
-                    if (extractProcess(jsonNode) == CWLProcess.WORKFLOW) {
-                        String currentId = jsonNode.get(ID).asText();
-                        if (currentId.startsWith("#")) {
-                            currentId = currentId.substring(1);
-                        }
-                        if (currentId.equals(packedWorkflowId)) {
-                            cwlFile = jsonNode;
-                            break;
+                boolean found = false;
+                if (cwlFile.has(DOC_GRAPH)) {
+                    for (JsonNode jsonNode : cwlFile.get(DOC_GRAPH)) {
+                        if (extractProcess(jsonNode) == CWLProcess.WORKFLOW) {
+                            String currentId = jsonNode.get(ID).asText();
+                            if (currentId.startsWith("#")) {
+                                currentId = currentId.substring(1);
+                            }
+                            if (currentId.equals(packedWorkflowId)) {
+                                cwlFile = jsonNode;
+                                found = true;
+                                break;
+                            }
                         }
                     }
                 }
+                if (!found) throw new WorkflowNotFoundException();
+            } else {
+                // Check the current json node is a workflow
+                if (extractProcess(cwlFile) != CWLProcess.WORKFLOW) {
+                    throw new WorkflowNotFoundException();
+                }
             }
 
             // Use filename for label if there is no defined one

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

@@ -19,6 +19,7 @@
 
 package org.commonwl.view.cwl;
 
+import org.apache.jena.query.QueryException;
 import org.commonwl.view.researchobject.ROBundleFactory;
 import org.commonwl.view.workflow.QueuedWorkflow;
 import org.commonwl.view.workflow.QueuedWorkflowRepository;
@@ -88,19 +89,22 @@ public void createWorkflowFromQueued(QueuedWorkflow queuedWorkflow, File workflo
 
             // Mark success on queue
             queuedWorkflow.setCwltoolStatus(CWLToolStatus.SUCCESS);
-            queuedWorkflowRepository.save(queuedWorkflow);
 
+        } catch (QueryException ex) {
+            logger.error("Jena query exception ", ex);
+            queuedWorkflow.setCwltoolStatus(CWLToolStatus.ERROR);
+            queuedWorkflow.setMessage("An error occurred when executing a query on the SPARQL store");
         } catch (CWLValidationException ex) {
             logger.error(ex.getMessage(), ex);
             queuedWorkflow.setCwltoolStatus(CWLToolStatus.ERROR);
             queuedWorkflow.setMessage(ex.getMessage());
-            queuedWorkflowRepository.save(queuedWorkflow);
         } catch (Exception ex) {
             logger.error("Unexpected error", ex);
             queuedWorkflow.setCwltoolStatus(CWLToolStatus.ERROR);
             queuedWorkflow.setMessage("Whoops! Cwltool ran successfully, but an unexpected " +
                     "error occurred in CWLViewer!\n" +
                     "Help us by reporting it on Gitter or a Github issue\n");
+        } finally {
             queuedWorkflowRepository.save(queuedWorkflow);
         }
 

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

@@ -506,7 +506,7 @@ private ModelAndView getWorkflow(GitDetails gitDetails, RedirectAttributes redir
                         logger.warn("git.notFound " + workflowForm, ex);
                         errors.rejectValue("url", "git.notFound", "The workflow could not be found within the repository");
                     } catch (IOException ex) {
-                        logger.warn("git.parsingError " + workflowForm, ex);
+                        logger.warn("url.parsingError " + workflowForm, ex);
                         errors.rejectValue("url", "url.parsingError", "The workflow could not be parsed from the given URL");
                     }
                 }