Remove done files after hashing failure/resume

Author: bbimber

singlecell/api-src/org/labkey/api/singlecell/pipeline/AbstractSingleCellPipelineStep.java

@@ -544,7 +544,7 @@ protected static File getSeuratErrorFile(SequenceOutputHandler.JobContext ctx)
         return new File(ctx.getOutputDir(), "seuratErrors.txt");
     }
 
-    protected void onFailure(SequenceOutputHandler.JobContext ctx) throws PipelineJobException
+    protected void onFailure(SequenceOutputHandler.JobContext ctx, String outputPrefix) throws PipelineJobException
     {
         // This allows subclasses to implement tool-specific failure handling
     }
@@ -559,7 +559,7 @@ private void handlePossibleFailure(SequenceOutputHandler.JobContext ctx, String
                 List<String> errors = IOUtils.readLines(Readers.getReader(errorFile));
                 errorFile.delete();
 
-                onFailure(ctx);
+                onFailure(ctx, outputPrefix);
 
                 File html = getExpectedHtmlFile(ctx, outputPrefix);
                 if (html.exists())

singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunCellHashing.java

@@ -72,9 +72,19 @@ public String getDockerContainerName()
     }
 
     @Override
-    protected void onFailure(SequenceOutputHandler.JobContext ctx) throws PipelineJobException
+    protected void onFailure(SequenceOutputHandler.JobContext ctx, String outputPrefix) throws PipelineJobException
     {
         copyHtmlLocally(ctx);
+
+        // Also delete the .done files, so hashing will repeat if we change params:
+        for (File f : ctx.getOutputDir().listFiles())
+        {
+            if (f.getName().endsWith(CellHashingServiceImpl.CALL_EXTENSION + ".done"))
+            {
+                ctx.getLogger().debug("Removing hashing .done file: " + f.getName());
+                f.delete();
+            }
+        }
     }
 
     private void copyHtmlLocally(SequenceOutputHandler.JobContext ctx) throws PipelineJobException