Debug job resume

Author: bbimber

singlecell/src/org/labkey/singlecell/analysis/ProcessSingleCellHandler.java

@@ -482,6 +482,7 @@ public static Resumer create(JobContext ctx) throws PipelineJobException
                 ret.setLocalWorkDir(ctx.getWorkDir().getDir());
                 ret._fileManager.onResume(ctx.getJob(), ctx.getWorkDir());
 
+                ctx.getLogger().debug("Cached steps: " + StringUtils.join(ret._stepOutputs.keySet(), ", "));
             }
 
             return ret;
@@ -499,7 +500,7 @@ public List<SingleCellStep.SeuratObjectWrapper> getSeuratFromStep(int stepIdx)
 
         public void setStepComplete(Logger log, SingleCellStep step, int stepIdx, RecordedAction action, List<SingleCellStep.SeuratObjectWrapper> seurat, File markdown, File html) throws PipelineJobException
         {
-            log.info("Marking step complete: " + step.getProvider().getName());
+            log.info("Marking step complete: " + step.getProvider().getName() + ", " + stepIdx);
 
             if (seurat != null)
             {
@@ -509,6 +510,11 @@ public void setStepComplete(Logger log, SingleCellStep step, int stepIdx, Record
             action.addOutput(markdown, "Markdown File", true);
             action.addOutput(html, "HTML Report", false);
 
+            if (_stepOutputs.containsKey(stepIdx))
+            {
+                log.debug("Step already marked as done: " + step.getProvider().getName() + " / " +stepIdx);
+            }
+
             _stepOutputs.put(stepIdx, seurat);
             _markdowns.put(stepIdx, markdown);
             _htmlFiles.put(stepIdx, html);