Allow readset jobs to operate on archived data

bbimber · bbimber · commit a475975985ef · 2022-01-27T15:51:33.000-08:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceReadsetHandlerInitTask.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceReadsetHandlerInitTask.java
@@ -75,7 +75,7 @@ private SequenceReadsetHandlerJob getPipelineJob()
         return (SequenceReadsetHandlerJob)getJob();
     }
 
-    @NotNull
+    @NotNull @Override
     public RecordedActionSet run() throws PipelineJobException
     {
         List<RecordedAction> actions = new ArrayList<>();
@@ -90,7 +90,8 @@ public RecordedActionSet run() throws PipelineJobException
                 throw new PipelineJobException("Readset not instanceof SequenceReadsetImpl");
             }
 
-            ((SequenceReadsetImpl)f).cacheForRemoteServer();
+
+            getPipelineJob().getSequenceSupport().cacheReadset(f.getReadsetId(), getJob().getUser(), handler.supportsSraArchivedData());
         }
 
         getJob().getLogger().info("total readsets: " + getPipelineJob().getReadsets().size());

Original file line number	Diff line number	Diff line change
`@@ -75,7 +75,7 @@ private SequenceReadsetHandlerJob getPipelineJob()`
`75`	`75`	`return (SequenceReadsetHandlerJob)getJob();`
`76`	`76`	`}`
`77`	`77`
`78`		`- @NotNull`
	`78`	`+ @NotNull @Override`
`79`	`79`	`public RecordedActionSet run() throws PipelineJobException`
`80`	`80`	`{`
`81`	`81`	`List<RecordedAction> actions = new ArrayList<>();`
`@@ -90,7 +90,8 @@ public RecordedActionSet run() throws PipelineJobException`
`90`	`90`	`throw new PipelineJobException("Readset not instanceof SequenceReadsetImpl");`
`91`	`91`	`}`
`92`	`92`
`93`		`- ((SequenceReadsetImpl)f).cacheForRemoteServer();`
	`93`	`+`
	`94`	`+ getPipelineJob().getSequenceSupport().cacheReadset(f.getReadsetId(), getJob().getUser(), handler.supportsSraArchivedData());`
`94`	`95`	`}`
`95`	`96`
`96`	`97`	`getJob().getLogger().info("total readsets: " + getPipelineJob().getReadsets().size());`