More visibility into orphan aligner indexes

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/OrphanFilePipelineJob.java

@@ -57,6 +57,8 @@
 import java.util.Map;
 import java.util.Set;
 
+import static org.labkey.sequenceanalysis.pipeline.SequenceTaskHelper.SHARED_SUBFOLDER_NAME;
+
 public class OrphanFilePipelineJob extends PipelineJob
 {
     // Default constructor for serialization
@@ -373,6 +375,16 @@ public void getOrphanFilesForContainer(Container c, User u, Set<File> orphanFile
                                 unexpectedPipelineDirs.add(subdir);
                             }
 
+                            File sharedDir = new File(subdir, SHARED_SUBFOLDER_NAME);
+                            if (sharedDir.exists())
+                            {
+                                long size = FileUtils.sizeOfDirectory(sharedDir);
+                                if (size > 1e6)
+                                {
+                                    getJob().getLogger().warn("Large Shared folder: " + sharedDir.getPath());
+                                }
+                            }
+
                             getOrphanFilesForDirectory(knownExpDatas, dataMap, subdir, orphanFiles, orphanIndexes);
                         }
                     }

SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceAlignmentTask.java

@@ -209,10 +209,6 @@ public WorkDirectory createWorkDirectory(String jobGUID, FileAnalysisJobSupport
         @Override
         public boolean isJobComplete(PipelineJob job)
         {
-            FileAnalysisJobSupport support = (FileAnalysisJobSupport) job;
-            String baseName = support.getBaseName();
-            File dirAnalysis = support.getAnalysisDirectory();
-
             return false;
         }
     }
@@ -469,6 +465,8 @@ else if (doCopy)
                 actions.add(action);
 
                 referenceGenome.setWorkingFasta(new File(targetDir, refFasta.getName()));
+
+                getTaskFileManagerImpl().addIntermediateFile(targetDir);
             }
             catch (IOException e)
             {