Script that compresses all Mongo DBs except admin and local.

gistfile1.js

var hospitals = db.getMongo().getDBNames();
for(var h in hospitals){
  if (hospitals[h] != "admin" && hospitals[h] != "local") {
    var db = db.getMongo().getDB( hospitals[h] );
    var size_before = ((db.stats()["dataSize"] / 60) / 60);
    print( "Repairing DB " + db.getName() + " - " + size_before );
    db.repairDatabase();
    var size = ((db.stats()["dataSize"] / 60) / 60);
    print( "  Complete - " + size + ".  Size reduced by " + ( size_before - size ) + " MB." );
  }
}
print( "Repair Process Complete" );