Bugfix GenomicsDbImport wrapper

bbimber · bbimber · commit 148871269b0a · 2021-06-15T10:35:13.000-07:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/AbstractGenomicsDBImportHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/AbstractGenomicsDBImportHandler.java
@@ -342,11 +342,13 @@ private void copyTopLevelFiles(PipelineJob job, File sourceWorkspace, File desti
             {
                 job.getLogger().debug("workspace file exists, will not overwrite: " + metaDirDest.getPath());
             }
-
-            FileUtils.deleteDirectory(metaDirDest);
+            else
+            {
+                FileUtils.deleteDirectory(metaDirDest);
+            }
         }
 
-        if (!metaDirDest.exists())
+        if (metaDir.exists() && !metaDirDest.exists())
         {
             job.getLogger().debug("Copying directory with rsync: " + metaDir.getPath());
             new SimpleScriptWrapper(job.getLogger()).execute(Arrays.asList(

Original file line number	Diff line number	Diff line change
`@@ -342,11 +342,13 @@ private void copyTopLevelFiles(PipelineJob job, File sourceWorkspace, File desti`
`342`	`342`	`{`
`343`	`343`	`job.getLogger().debug("workspace file exists, will not overwrite: " + metaDirDest.getPath());`
`344`	`344`	`}`
`345`		`-`
`346`		`- FileUtils.deleteDirectory(metaDirDest);`
	`345`	`+ else`
	`346`	`+ {`
	`347`	`+ FileUtils.deleteDirectory(metaDirDest);`
	`348`	`+ }`
`347`	`349`	`}`
`348`	`350`
`349`		`- if (!metaDirDest.exists())`
	`351`	`+ if (metaDir.exists() && !metaDirDest.exists())`
`350`	`352`	`{`
`351`	`353`	`job.getLogger().debug("Copying directory with rsync: " + metaDir.getPath());`
`352`	`354`	`new SimpleScriptWrapper(job.getLogger()).execute(Arrays.asList(`