Allow readset handlers to work on archived data

Author: bbimber

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/SequenceOutputHandler.java

@@ -85,6 +85,11 @@ default boolean requiresGenome()
 
     public boolean canProcess(SequenceOutputFile o);
 
+    default boolean supportsSraArchivedData()
+    {
+        return false;
+    }
+
     /**
      * If false, this handler will not be returned with the list of available handlers for a given set of files.
      * This allows the developer to register handlers that feed into the pipeline, but can only be called through specific code/UI

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

@@ -3546,7 +3546,7 @@ private JSONObject getDataJsonForReadset(SequenceOutputHandler handler, Readset
             o.put("totalReadData", rs.getReadData().size());
             for (ReadData rd : rs.getReadData())
             {
-                if (rd.isArchived())
+                if (rd.isArchived() && !handler.supportsSraArchivedData())
                 {
                     o.put("fileExists", false);
                     o.put("isArchived", true);
@@ -3557,19 +3557,25 @@ private JSONObject getDataJsonForReadset(SequenceOutputHandler handler, Readset
                 ExpData d = rd.getFileId1() == 0 ? null : ExperimentService.get().getExpData(rd.getFileId1());
                 if (d == null || d.getFile() == null || !d.getFile().exists())
                 {
-                    o.put("fileExists", false);
-                    o.put("error", true);
-                    return o;
+                    if (!handler.supportsSraArchivedData())
+                    {
+                        o.put("fileExists", false);
+                        o.put("error", true);
+                        return o;
+                    }
                 }
 
                 if (rd.getFileId2() != null)
                 {
                     d = rd.getFileId2() == 0 ? null : ExperimentService.get().getExpData(rd.getFileId2());
                     if (d == null || d.getFile() == null || !d.getFile().exists())
                     {
-                        o.put("fileExists", false);
-                        o.put("error", true);
-                        return o;
+                        if (!handler.supportsSraArchivedData())
+                        {
+                            o.put("fileExists", false);
+                            o.put("error", true);
+                            return o;
+                        }
                     }
                 }
             }

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/RestoreSraDataHandler.java

@@ -66,6 +66,12 @@ public boolean canProcess(SequenceOutputFile o)
         return false;
     }
 
+    @Override
+    public boolean supportsSraArchivedData()
+    {
+        return true;
+    }
+
     @Override
     public boolean doRunRemote()
     {