Improved logging on slurm execution errors

Author: bbimber

cluster/src/org/labkey/cluster/pipeline/AbstractClusterExecutionEngine.java

@@ -725,7 +725,11 @@ protected List<String> execute(String command)
                 String output = IOUtils.toString(p.getInputStream(), StringUtilsLabKey.DEFAULT_CHARSET);
                 String errorOutput = IOUtils.toString(p.getErrorStream(), StringUtilsLabKey.DEFAULT_CHARSET);
 
-                p.waitFor();
+                int exitCode = p.waitFor();
+                if (exitCode != 0)
+                {
+                    _log.error("Non-zero exit from command: " + command);
+                }
 
                 if (errorOutput != null)
                 {

cluster/src/org/labkey/cluster/pipeline/SlurmExecutionEngine.java

@@ -88,6 +88,10 @@ protected List<String> submitJobToCluster(ClusterJob j, PipelineJob job) throws
                 }
             }
         }
+        else
+        {
+            _log.info("No output returned after slurm command: " + command);
+        }
 
         if (j.getClusterId() == null)
         {

singlecell/resources/web/singlecell/panel/SingleCellProcessingPanel.js

@@ -78,7 +78,7 @@ Ext4.define('SingleCell.panel.SingleCellProcessingPanel', {
                         useOutputFileContainer.setValue(val !== 'individual');
                     }
                 },
-                value: null,
+                value: this.outputFileIds.size === 1 ? 'individual' : null,
                 allowBlank: false
             },{
                 xtype: 'checkbox',