Fix issue related to JSONObject migration

bbimber · bbimber · commit 543aa91f29ad · 2023-06-02T15:12:24.000-07:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/ScatterGatherUtils.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/ScatterGatherUtils.java
@@ -38,9 +38,9 @@ public static void possiblyCacheSupportFiles(SequenceOutputHandler.JobContext ct
     {
         for (String param : Arrays.asList("exclude_intervals", "forceSitesFile"))
         {
-            if (ctx.getParams().get("variantCalling.GenotypeGVCFs." + param) != null)
+            if (!ctx.getParams().isNull("variantCalling.GenotypeGVCFs." + param))
             {
-                File inputFile = ctx.getSequenceSupport().getCachedData(ctx.getParams().getInt("variantCalling.GenotypeGVCFs." + param));
+                File inputFile = ctx.getSequenceSupport().getCachedData(ctx.getParams().optInt("variantCalling.GenotypeGVCFs." + param));
                 if (!inputFile.exists())
                 {
                     throw new PipelineJobException("Unable to find file: " + inputFile.getPath());

Original file line number	Diff line number	Diff line change
`@@ -38,9 +38,9 @@ public static void possiblyCacheSupportFiles(SequenceOutputHandler.JobContext ct`
`38`	`38`	`{`
`39`	`39`	`for (String param : Arrays.asList("exclude_intervals", "forceSitesFile"))`
`40`	`40`	`{`
`41`		`- if (ctx.getParams().get("variantCalling.GenotypeGVCFs." + param) != null)`
	`41`	`+ if (!ctx.getParams().isNull("variantCalling.GenotypeGVCFs." + param))`
`42`	`42`	`{`
`43`		`- File inputFile = ctx.getSequenceSupport().getCachedData(ctx.getParams().getInt("variantCalling.GenotypeGVCFs." + param));`
	`43`	`+ File inputFile = ctx.getSequenceSupport().getCachedData(ctx.getParams().optInt("variantCalling.GenotypeGVCFs." + param));`
`44`	`44`	`if (!inputFile.exists())`
`45`	`45`	`{`
`46`	`46`	`throw new PipelineJobException("Unable to find file: " + inputFile.getPath());`