Only use visible tracks when determining the default tracks for a JBrowse session

Author: bbimber

jbrowse/src/org/labkey/jbrowse/model/JBrowseSession.java

@@ -244,17 +244,19 @@ public JSONObject getConfigJson(User u, Logger log) throws PipelineJobException
 
         JSONArray tracks = new JSONArray();
         List<JsonFile> jsonFiles = getJsonFiles(u, false);
+        List<JsonFile> visibleTracks = new ArrayList<>();
         for (JsonFile jsonFile : jsonFiles)
         {
             JSONObject o = jsonFile.toTrackJson(u, rg, log);
             if (o != null)
             {
                 tracks.put(o);
+                visibleTracks.add(jsonFile);
             }
         }
 
         ret.put("tracks", tracks);
-        ret.put("defaultSession", getDefaultSessionJson(jsonFiles));
+        ret.put("defaultSession", getDefaultSessionJson(visibleTracks));
 
         return ret;
     }