Bugfix to GenomicsDbImport when genomicsdbSegmentSize is null

bbimber · bbimber · commit 05a1a91a3bec · 2022-03-16T21:50:53.000-07:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/AbstractGenomicsDBImportHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/AbstractGenomicsDBImportHandler.java
@@ -765,7 +765,7 @@ private void doConsolidate(JobContext ctx, File workingDestinationWorkspaceFolde
             baseArgs.add("--shared-posixfs-optimizations");
         }
 
-        if (ctx.getParams().get("genomicsdbSegmentSize") != null)
+        if (StringUtils.trimToNull(ctx.getParams().optString("genomicsdbSegmentSize")) != null)
         {
             baseArgs.add("--segment-size");
             baseArgs.add(String.valueOf(ctx.getParams().get("genomicsdbSegmentSize")));

Original file line number	Diff line number	Diff line change
`@@ -765,7 +765,7 @@ private void doConsolidate(JobContext ctx, File workingDestinationWorkspaceFolde`
`765`	`765`	`baseArgs.add("--shared-posixfs-optimizations");`
`766`	`766`	`}`
`767`	`767`
`768`		`- if (ctx.getParams().get("genomicsdbSegmentSize") != null)`
	`768`	`+ if (StringUtils.trimToNull(ctx.getParams().optString("genomicsdbSegmentSize")) != null)`
`769`	`769`	`{`
`770`	`770`	`baseArgs.add("--segment-size");`
`771`	`771`	`baseArgs.add(String.valueOf(ctx.getParams().get("genomicsdbSegmentSize")));`