Bugfix to readset import when one pair is archived to SRA

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/ReadDataImpl.java

@@ -201,18 +201,28 @@ public void setModifiedBy(Integer modifiedBy)
         _modifiedBy = modifiedBy;
     }
 
+    public File getFile1(boolean allowArchived)
+    {
+        return getFile(1, _fileId1, allowArchived);
+    }
+
     @Override
     @Transient
     public File getFile1()
     {
-        return getFile(1, _fileId1);
+        return getFile1(false);
     }
 
     @Override
     @Transient
     public File getFile2()
     {
-        return getFile(2, _fileId2);
+        return getFile2(false);
+    }
+
+    public File getFile2(boolean allowArchived)
+    {
+        return getFile(2, _fileId2, false);
     }
 
     public void setFile(File f, int fileIdx)
@@ -248,9 +258,9 @@ public Integer getTotalReads()
     }
 
     @Transient
-    private File getFile(int fileIdx, Integer fileId)
+    private File getFile(int fileIdx, Integer fileId, boolean allowArchived)
     {
-        if (isArchived())
+        if (isArchived() && !allowArchived)
         {
             return null;
         }

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

@@ -505,10 +505,10 @@ private void checkForDuplicateFileNames(List<SequenceReadsetImpl> readsets, List
             {
                 Map<String, File> existingFileNames = new HashMap<>();
                 preexistingReadData.forEach(rd -> {
-                    existingFileNames.put(rd.getFile1().getName(), rd.getFile1());
+                    existingFileNames.put(rd.getFile1(true).getName(), rd.getFile1(true));
                     if (rd.getFile2() != null)
                     {
-                        existingFileNames.put(rd.getFile2().getName(), rd.getFile2());
+                        existingFileNames.put(rd.getFile2(true).getName(), rd.getFile2(true));
                     }
                 });