Fix issue when using temporary genome in combination with genome caching

bbimber · bbimber · commit 765197249312 · 2023-05-26T14:39:35.000-07:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ReferenceGenomeImpl.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ReferenceGenomeImpl.java
@@ -61,7 +61,7 @@ public boolean isTemporaryGenome() {
     @Override
     public @NotNull File getWorkingFastaFile()
     {
-        if (SequencePipelineService.get().isRemoteGenomeCacheUsed())
+        if (!isTemporaryGenome() && SequencePipelineService.get().isRemoteGenomeCacheUsed())
         {
             File ret = SequencePipelineService.get().getRemoteGenomeCacheDirectory();
             if (ret != null)

Original file line number	Diff line number	Diff line change
`@@ -61,7 +61,7 @@ public boolean isTemporaryGenome() {`
`61`	`61`	`@Override`
`62`	`62`	`public @NotNull File getWorkingFastaFile()`
`63`	`63`	`{`
`64`		`- if (SequencePipelineService.get().isRemoteGenomeCacheUsed())`
	`64`	`+ if (!isTemporaryGenome() && SequencePipelineService.get().isRemoteGenomeCacheUsed())`
`65`	`65`	`{`
`66`	`66`	`File ret = SequencePipelineService.get().getRemoteGenomeCacheDirectory();`
`67`	`67`	`if (ret != null)`