Bugfix to readset import when one pair is archived to SRA

BimberLab · Aug 30, 2024 · cb09960 · cb09960
1 parent cf1fa97
commit cb09960
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Showing 2 changed files with 4 additions and 2 deletions.
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ReadsetInitTask.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ReadsetInitTask.java
@@ -218,7 +218,9 @@ public RecordedActionSet run() throws PipelineJobException
             for (SequenceReadsetImpl rs : readsets)
             {
                 getJob().getLogger().debug("caching readset: " + rs.getName() + " with " + rs.getReadData().size() + " files");
-                getPipelineJob().getSequenceSupport().cacheReadset(rs);
+
+                // NOTE: allow archived data
+                getPipelineJob().getSequenceSupport().cacheReadset(rs, true);
             }
         }
         catch (IOException e)

diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceNormalizationTask.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceNormalizationTask.java
@@ -626,7 +626,7 @@ else if (lane.isEmpty())
 
                     if (rd.isEmpty())
                     {
-                        getJob().getLogger().warn("no file groups found ofr rs: " + rs.getName() + " with fileGroupId: " + rs.getFileSetName());
+                        getJob().getLogger().warn("no file groups found for readset: " + rs.getName() + " with fileGroupId: " + rs.getFileSetName());
                     }
 
                     rs.setReadData(rd);