Merge branch 'develop' of github.com:SeqWare/seqware into develop

Former-commit-id: cab0c58

Author: denis-yuen

seqware-pipeline/src/main/java/io/seqware/WorkflowRuns.java

@@ -4,6 +4,9 @@
 import net.sourceforge.seqware.common.metadata.MetadataFactory;
 import net.sourceforge.seqware.common.model.WorkflowRun;
 import net.sourceforge.seqware.common.model.WorkflowRunStatus;
+import static net.sourceforge.seqware.common.model.WorkflowRunStatus.pending;
+import static net.sourceforge.seqware.common.model.WorkflowRunStatus.running;
+import static net.sourceforge.seqware.common.model.WorkflowRunStatus.submitted;
 import net.sourceforge.seqware.common.util.configtools.ConfigTools;
 
 public class WorkflowRuns {
@@ -25,6 +28,13 @@ public static void submitCancel(int workflowRunAccession) {
                                               + wr.getWorkflowEngine());
     }
   }
+  
+  public static void failWorkflow(int workflowRunAccession) {
+    Metadata md = MetadataFactory.get(ConfigTools.getSettings());
+    WorkflowRun wr = md.getWorkflowRun(workflowRunAccession);
+    wr.setStatus(WorkflowRunStatus.failed);
+    md.updateWorkflowRun(wr);
+  }
 
   public static void submitRetry(int workflowRunAccession) {
     Metadata md = MetadataFactory.get(ConfigTools.getSettings());

seqware-pipeline/src/main/java/net/sourceforge/seqware/pipeline/plugin/WorkflowPlugin.java

@@ -11,6 +11,7 @@
  */
 package net.sourceforge.seqware.pipeline.plugin;
 
+import io.seqware.WorkflowRuns;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
@@ -521,7 +522,10 @@ public static ReturnValue launchNewWorkflow(OptionSet options, Map<String, Strin
         workflowEngine = dataModel.getWorkflow_engine();
       }
     } catch (Exception e) {
-      Log.fatal(e, e);
+      if (workflowRunAccession != null){
+        Log.fatal("Exception constructing data model, failing workflow " + workflowRunAccession, e);
+        WorkflowRuns.failWorkflow(workflowRunAccession);
+      }
       ret.setExitStatus(ReturnValue.INVALIDARGUMENT);
       return ret;
     }

seqware-pipeline/src/main/java/net/sourceforge/seqware/pipeline/workflowV2/WorkflowDataModelFactory.java

@@ -18,6 +18,7 @@
 import net.sourceforge.seqware.common.model.WorkflowRun;
 import net.sourceforge.seqware.common.module.ReturnValue;
 import net.sourceforge.seqware.common.util.Log;
+import net.sourceforge.seqware.common.util.Rethrow;
 import net.sourceforge.seqware.common.util.maptools.MapTools;
 import net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo;
 import net.sourceforge.seqware.pipeline.bundle.Bundle;
@@ -247,15 +248,20 @@ public AbstractWorkflowDataModel getWorkflowDataModel(Integer workflowAccession,
                 m = clazz.getMethod("buildWorkflow");
                 m.invoke(dataModel);
             } catch (SecurityException e) {
-                Log.error(e);
+                Log.error("SecurityException",e);
+                Rethrow.rethrow(e);
             } catch (NoSuchMethodException e) {
-                Log.error(e);
+                Log.error("NoSuchMethodException",e);
+                Rethrow.rethrow(e);
             } catch (IllegalArgumentException e) {
-                Log.error(e);
+                Log.error("IllegalArgumentException",e);
+                Rethrow.rethrow(e);
             } catch (IllegalAccessException e) {
-                Log.error(e);
+                Log.error("IllegalAccessException",e);
+                Rethrow.rethrow(e);
             } catch (InvocationTargetException e) {
-                Log.error(e);
+                Log.error("InvocationTargetException",e);
+                Rethrow.rethrow(e);
             }
         } else {
             WorkflowXmlParser xmlParser = new WorkflowXmlParser();