Debug singleR dual output issue

bbimber · bbimber · commit 187dd75f29c5 · 2023-01-04T09:22:02.000-08:00
diff --git a/singlecell/api-src/org/labkey/api/singlecell/pipeline/AbstractSingleCellPipelineStep.java b/singlecell/api-src/org/labkey/api/singlecell/pipeline/AbstractSingleCellPipelineStep.java
@@ -46,6 +46,13 @@ public Output execute(SequenceOutputHandler.JobContext ctx, List<SeuratObjectWra
     {
         SingleCellOutput output = new SingleCellOutput();
 
+        File tracker = new File(ctx.getOutputDir(), "savedSeuratObjects.txt");
+        if (tracker.exists())
+        {
+            ctx.getLogger().debug("deleting pre-existing file: " + tracker.getName());
+            tracker.delete();
+        }
+
         File rmd = createRmd(output, ctx, inputObjects, outputPrefix);
         if (hasCompleted())
         {
@@ -74,7 +81,6 @@ public Output execute(SequenceOutputHandler.JobContext ctx, List<SeuratObjectWra
         output.setHtmlFile(htmlFile);
 
         List<SeuratObjectWrapper> outputs = new ArrayList<>();
-        File tracker = new File(ctx.getOutputDir(), "savedSeuratObjects.txt");
         if (!tracker.exists())
         {
             throw new PipelineJobException("File not found: " + tracker.getPath());

Original file line number	Diff line number	Diff line change
`@@ -46,6 +46,13 @@ public Output execute(SequenceOutputHandler.JobContext ctx, List<SeuratObjectWra`
`46`	`46`	`{`
`47`	`47`	`SingleCellOutput output = new SingleCellOutput();`
`48`	`48`
	`49`	`+ File tracker = new File(ctx.getOutputDir(), "savedSeuratObjects.txt");`
	`50`	`+ if (tracker.exists())`
	`51`	`+ {`
	`52`	`+ ctx.getLogger().debug("deleting pre-existing file: " + tracker.getName());`
	`53`	`+ tracker.delete();`
	`54`	`+ }`
	`55`	`+`
`49`	`56`	`File rmd = createRmd(output, ctx, inputObjects, outputPrefix);`
`50`	`57`	`if (hasCompleted())`
`51`	`58`	`{`
`@@ -74,7 +81,6 @@ public Output execute(SequenceOutputHandler.JobContext ctx, List<SeuratObjectWra`
`74`	`81`	`output.setHtmlFile(htmlFile);`
`75`	`82`
`76`	`83`	`List<SeuratObjectWrapper> outputs = new ArrayList<>();`
`77`		`- File tracker = new File(ctx.getOutputDir(), "savedSeuratObjects.txt");`
`78`	`84`	`if (!tracker.exists())`
`79`	`85`	`{`
`80`	`86`	`throw new PipelineJobException("File not found: " + tracker.getPath());`