Cannot call getUser() on remote pipelines

bbimber · bbimber · commit 6608a70e202a · 2023-11-09T13:54:37.000-08:00
diff --git a/singlecell/src/org/labkey/singlecell/run/NimbleHelper.java b/singlecell/src/org/labkey/singlecell/run/NimbleHelper.java
@@ -184,7 +184,7 @@ private File getGenomeCsv(int genomeId) throws PipelineJobException
 
     private File getGenomeCsv(int genomeId, boolean forceWorkDir) throws PipelineJobException
     {
-        ReferenceGenome rg = SequenceAnalysisService.get().getReferenceGenome(genomeId, getPipelineCtx().getJob().getUser());
+        ReferenceGenome rg = getPipelineCtx().getSequenceSupport().getCachedGenome(genomeId);
         if (rg == null)
         {
             throw new PipelineJobException("Unable to find genome: " + genomeId);
@@ -206,7 +206,7 @@ private File getGenomeFasta(int genomeId) throws PipelineJobException
 
     private File getGenomeFasta(int genomeId, boolean forceWorkDir) throws PipelineJobException
     {
-        ReferenceGenome rg = SequenceAnalysisService.get().getReferenceGenome(genomeId, getPipelineCtx().getJob().getUser());
+        ReferenceGenome rg = getPipelineCtx().getSequenceSupport().getCachedGenome(genomeId);
         if (rg == null)
         {
             throw new PipelineJobException("Unable to find genome: " + genomeId);

Original file line number	Diff line number	Diff line change
`@@ -184,7 +184,7 @@ private File getGenomeCsv(int genomeId) throws PipelineJobException`
`184`	`184`
`185`	`185`	`private File getGenomeCsv(int genomeId, boolean forceWorkDir) throws PipelineJobException`
`186`	`186`	`{`
`187`		`- ReferenceGenome rg = SequenceAnalysisService.get().getReferenceGenome(genomeId, getPipelineCtx().getJob().getUser());`
	`187`	`+ ReferenceGenome rg = getPipelineCtx().getSequenceSupport().getCachedGenome(genomeId);`
`188`	`188`	`if (rg == null)`
`189`	`189`	`{`
`190`	`190`	`throw new PipelineJobException("Unable to find genome: " + genomeId);`
`@@ -206,7 +206,7 @@ private File getGenomeFasta(int genomeId) throws PipelineJobException`
`206`	`206`
`207`	`207`	`private File getGenomeFasta(int genomeId, boolean forceWorkDir) throws PipelineJobException`
`208`	`208`	`{`
`209`		`- ReferenceGenome rg = SequenceAnalysisService.get().getReferenceGenome(genomeId, getPipelineCtx().getJob().getUser());`
	`209`	`+ ReferenceGenome rg = getPipelineCtx().getSequenceSupport().getCachedGenome(genomeId);`
`210`	`210`	`if (rg == null)`
`211`	`211`	`{`
`212`	`212`	`throw new PipelineJobException("Unable to find genome: " + genomeId);`