Allow ReadsetHandlerJob to act on the correct set of inputs

Author: bbimber

.github/workflows/build.yml

@@ -1,7 +1,10 @@
 name: Build DISCVR
 on:
+  workflow_dispatch:
   push:
   pull_request:
+  schedule:
+    - cron: '0 3 * * *'
 jobs:
   build-modules:
     # See: https://help.github.com/en/actions/reference/contexts-and-expression-syntax-for-github-actions#github-context

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

@@ -19,13 +19,15 @@
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.stream.Collectors;
 
 /**
  * Created by bimber on 1/16/2015.
  */
 public class SequenceReadsetHandlerJob extends SequenceJob implements HasJobParams
 {
     private String _handlerClassName;
+    private List<Integer> _readsetIds;
 
     // Default constructor for serialization
     protected SequenceReadsetHandlerJob()
@@ -39,9 +41,11 @@ public SequenceReadsetHandlerJob(Container c, User user, @Nullable String jobNam
         _handlerClassName = handler.getClass().getName();
 
         //for the purpose of caching files:
+        _readsetIds = new ArrayList<>();
         for (SequenceReadsetImpl rs : readsets)
         {
             getSequenceSupport().cacheReadset(rs);
+            _readsetIds.add(rs.getReadsetId());
         }
     }
 
@@ -64,7 +68,7 @@ public SequenceOutputHandler<SequenceOutputHandler.SequenceReadsetProcessor> get
 
     public List<Readset> getReadsets()
     {
-        return getSequenceSupport().getCachedReadsets();
+        return getReadsetIds().stream().map(getSequenceSupport()::getCachedReadset).collect(Collectors.toList());
     }
 
     @Override
@@ -94,4 +98,14 @@ public List<File> getInputFiles()
 
         return null;
     }
+
+    public List<Integer> getReadsetIds()
+    {
+        return _readsetIds;
+    }
+
+    public void setReadsetIds(List<Integer> readsetIds)
+    {
+        _readsetIds = readsetIds;
+    }
 }