detect non-Workflow CWL documents and give a better error message

Author: mr-c

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

@@ -0,0 +1,36 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+
+package org.commonwl.view.cwl;
+
+/** Exception thrown when the provided CWL document is not a Workflow. */
+public class CWLNotAWorkflowException extends CWLValidationException {
+
+  public CWLNotAWorkflowException(String message) {
+    super(message);
+  }
+
+  public CWLNotAWorkflowException(Throwable throwable) {
+    super(throwable);
+  }
+
+  public CWLNotAWorkflowException(String message, Throwable throwable) {
+    super(message, throwable);
+  }
+}

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

@@ -181,7 +181,8 @@ public List<WorkflowOverview> getWorkflowOverviewsFromPacked(File packedFile) th
    * @return The constructed workflow object
    */
   public Workflow parseWorkflowNative(
-      InputStream workflowStream, String packedWorkflowId, String defaultLabel) throws IOException {
+      InputStream workflowStream, String packedWorkflowId, String defaultLabel)
+      throws IOException, WorkflowNotFoundException, CWLValidationException {
     // Parse file as yaml
     Map<String, Object> cwlFile = yamlStreamToJson(workflowStream);
 
@@ -205,9 +206,11 @@ public Workflow parseWorkflowNative(
       }
       if (!found && !packedWorkflowId.isEmpty()) throw new WorkflowNotFoundException();
     }
-    if (!found && extractProcess(cwlFile) == CWLProcess.WORKFLOW) {
-      // Check the current json node is a workflow
+    if (!found && (extractProcess(cwlFile) == CWLProcess.WORKFLOW)) {
       found = true;
+    } else if (found && (extractProcess(cwlFile) != CWLProcess.WORKFLOW)) {
+      throw new CWLNotAWorkflowException(
+          "Not a 'class: Workflow' CWL document, is a " + extractProcess(cwlFile));
     }
     if (!found) {
       throw new WorkflowNotFoundException();
@@ -248,7 +251,7 @@ public Workflow parseWorkflowNative(
    * @return The constructed workflow object
    */
   public Workflow parseWorkflowNative(Path workflowFile, String packedWorkflowId)
-      throws IOException {
+      throws IOException, WorkflowNotFoundException, CWLValidationException {
 
     // Check file size limit before parsing
     long fileSizeBytes = Files.size(workflowFile);

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

@@ -30,8 +30,10 @@
 import java.util.List;
 import org.apache.commons.lang.StringUtils;
 import org.commonwl.view.WebConfig;
+import org.commonwl.view.cwl.CWLNotAWorkflowException;
 import org.commonwl.view.cwl.CWLService;
 import org.commonwl.view.cwl.CWLToolStatus;
+import org.commonwl.view.cwl.CWLValidationException;
 import org.commonwl.view.git.GitDetails;
 import org.commonwl.view.graphviz.GraphVizService;
 import org.eclipse.jgit.api.errors.GitAPIException;
@@ -163,6 +165,10 @@ public ModelAndView createWorkflow(
           logger.warn("git.notFound " + workflowForm, ex);
           bindingResult.rejectValue("url", "git.notFound");
           return new ModelAndView("index");
+        } catch (CWLNotAWorkflowException ex) {
+          logger.warn("cwl.notAWorkflow " + workflowForm, ex);
+          bindingResult.rejectValue("url", "cwl.notAWorkflow");
+          return new ModelAndView("index");
         } catch (Exception ex) {
           logger.warn("url.parsingError " + workflowForm, ex);
           bindingResult.rejectValue("url", "url.parsingError");
@@ -629,7 +635,11 @@ private ModelAndView getWorkflow(GitDetails gitDetails, RedirectAttributes redir
           } catch (WorkflowNotFoundException ex) {
             logger.warn("git.notFound " + workflowForm, ex);
             errors.rejectValue(
-                "url", "git.notFound", "The workflow could not be found within the repository");
+                "url", "git.notFound", "The workflow could not be found within the repository.");
+          } catch (CWLValidationException ex) {
+            logger.warn("cwl.invalid " + workflowForm, ex);
+            errors.rejectValue(
+                "url", "cwl.invalid", "The workflow had a parsing error: " + ex.getMessage());
           } catch (IOException ex) {
             logger.warn("url.parsingError " + workflowForm, ex);
             errors.rejectValue(
@@ -658,7 +668,8 @@ private ModelAndView getWorkflow(GitDetails gitDetails, RedirectAttributes redir
     }
   }
 
-  private Resource getGraphFromInputStream(InputStream in, String format) throws IOException {
+  private Resource getGraphFromInputStream(InputStream in, String format)
+      throws IOException, WorkflowNotFoundException, CWLValidationException {
     Workflow workflow =
         cwlService.parseWorkflowNative(in, null, "workflow"); // first workflow will do
     InputStream out = graphVizService.getGraphStream(workflow.getVisualisationDot(), format);

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

@@ -33,6 +33,7 @@
 import org.commonwl.view.cwl.CWLService;
 import org.commonwl.view.cwl.CWLToolRunner;
 import org.commonwl.view.cwl.CWLToolStatus;
+import org.commonwl.view.cwl.CWLValidationException;
 import org.commonwl.view.git.GitDetails;
 import org.commonwl.view.git.GitSemaphore;
 import org.commonwl.view.git.GitService;
@@ -308,7 +309,7 @@ public File getROBundle(GitDetails gitDetails) throws ROBundleNotFoundException
    * @throws IOException Other file handling exceptions
    */
   public QueuedWorkflow createQueuedWorkflow(GitDetails gitInfo)
-      throws GitAPIException, WorkflowNotFoundException, IOException {
+      throws GitAPIException, WorkflowNotFoundException, IOException, CWLValidationException {
     QueuedWorkflow queuedWorkflow;
 
     Git repo = null;
@@ -338,7 +339,7 @@ public QueuedWorkflow createQueuedWorkflow(GitDetails gitInfo)
 
       // Check workflow is readable
       if (!Files.isReadable(workflowFile)) {
-        throw new WorkflowNotFoundException();
+        throw new WorkflowNotFoundException("Unable to read workflow file on disk.");
       }
 
       // Handling of packed workflows

src/main/resources/messages.properties

@@ -6,5 +6,8 @@ git.retrievalError = The workflow could not be retrieved from the Git repository
 git.notFound = The workflow could not be found within the repository
 git.sshError = SSH URLs are not supported, please provide a HTTPS URL for the repository or submodules
 
+cwl.invalid = An error with the CWL workflow itself
+cwl.notAWorkflow = The provided CWL document is not a "class: Workflow" file.
+
 url.parsingError = An unexpected error occurred when parsing the workflow
 url.noWorkflowsInDirectory = No workflow files were found in the given directory