Bug related to serializing HashMap

bbimber · bbimber · commit 32a6d5ff87c6 · 2025-12-17T13:07:35.000-08:00
diff --git a/singlecell/src/org/labkey/singlecell/run/NimbleAlignmentStep.java b/singlecell/src/org/labkey/singlecell/run/NimbleAlignmentStep.java
@@ -116,7 +116,7 @@ private File createNimbleBam(AlignmentOutputImpl output, Readset rs, List<File>
 
     private File getCachedLoupeFile(Readset rs, boolean throwIfNotFound) throws PipelineJobException
     {
-        Map<Long, Long> map = getPipelineCtx().getSequenceSupport().getCachedObject(CACHE_KEY, PipelineJob.createObjectMapper().getTypeFactory().constructParametricType(Map.class, Long.class, Long.class));
+        Map<Long, Long> map = getPipelineCtx().getSequenceSupport().getCachedObject(CACHE_KEY, PipelineJob.createObjectMapper().getTypeFactory().constructParametricType(HashMap.class, Long.class, Long.class));
         Long dataId = map.get(rs.getReadsetId());
         if (dataId == null)
         {

Original file line number	Diff line number	Diff line change
`@@ -116,7 +116,7 @@ private File createNimbleBam(AlignmentOutputImpl output, Readset rs, List<File>`
`116`	`116`
`117`	`117`	`private File getCachedLoupeFile(Readset rs, boolean throwIfNotFound) throws PipelineJobException`
`118`	`118`	`{`
`119`		`- Map<Long, Long> map = getPipelineCtx().getSequenceSupport().getCachedObject(CACHE_KEY, PipelineJob.createObjectMapper().getTypeFactory().constructParametricType(Map.class, Long.class, Long.class));`
	`119`	`+ Map<Long, Long> map = getPipelineCtx().getSequenceSupport().getCachedObject(CACHE_KEY, PipelineJob.createObjectMapper().getTypeFactory().constructParametricType(HashMap.class, Long.class, Long.class));`
`120`	`120`	`Long dataId = map.get(rs.getReadsetId());`
`121`	`121`	`if (dataId == null)`
`122`	`122`	`{`