Allow certain SequenceJob types to use archived readsets

BimberLab · Feb 16, 2024 · 86aa509 · 86aa509
1 parent 19d6779
commit 86aa509
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Showing 4 changed files with 18 additions and 1 deletion.
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/AlignmentAnalysisJob.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/AlignmentAnalysisJob.java
@@ -113,6 +113,12 @@ public static List<AlignmentAnalysisJob> createForAnalyses(Container c, User u,
         return ret;
     }
 
+    @Override
+    protected boolean shouldAllowArchivedReadsets()
+    {
+        return false;
+    }
+
     public static String NAME = "AlignmentAnalysisPipeline";
 
     public static void register() throws CloneNotSupportedException

diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceAlignmentJob.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceAlignmentJob.java
@@ -50,7 +50,7 @@ private SequenceAlignmentJob(Container c, User u, String jobName, PipeRoot root,
         super(SequencePipelineProvider.NAME, c, u, jobName, root, params, new TaskId(FileAnalysisTaskPipeline.class, NAME), FOLDER_NAME);
 
         _readsetId = readset.getRowId();
-        getSequenceSupport().cacheReadset(readset);
+        getSequenceSupport().cacheReadset(readset, shouldAllowArchivedReadsets());
         writeSupportToDisk();
     }
 

diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceJob.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceJob.java
@@ -110,6 +110,11 @@ protected SequenceJob(SequenceJob parentJob, String jobName, String subdirectory
         writeSupportToDisk();
     }
 
+    protected boolean shouldAllowArchivedReadsets()
+    {
+        return false;
+    }
+
     public SequenceJob(String providerName, Container c, User u, @Nullable String jobName, PipeRoot pipeRoot, JSONObject params, TaskId taskPipelineId, String folderPrefix) throws IOException
     {
         super(providerName, new ViewBackgroundInfo(c, u, null), pipeRoot);

diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceOutputHandlerJob.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceOutputHandlerJob.java
@@ -90,6 +90,12 @@ protected void saveFiles(List<SequenceOutputFile> files) throws IOException
         }
     }
 
+    @Override
+    protected boolean shouldAllowArchivedReadsets()
+    {
+        return true;
+    }
+
     protected List<SequenceOutputFile> readOutputFilesFromFile() throws PipelineJobException, IOException
     {
         File xml = getSerializedOutputFilesFile();