Fix MongoDB deprecation warnings

[osteele]

$ python -m unittest -q
/Users/osteele/code/htl2/ABE/.direnv/python-3.6.5/lib/python3.6/site-packages/mongoengine/document.py:428: DeprecationWarning: save is deprecated. Use insert_one or replace_one instead
  object_id = collection.save(doc, **write_concern)
/Users/osteele/code/htl2/ABE/.direnv/python-3.6.5/lib/python3.6/site-packages/mongoengine/queryset/queryset.py:51: DeprecationWarning: generator 'QuerySet._iter_results' raised StopIteration
  list(self._iter_results())
/Users/osteele/code/htl2/ABE/.direnv/python-3.6.5/lib/python3.6/site-packages/mongoengine/queryset/base.py:514: DeprecationWarning: update is deprecated. Use replace_one, update_one or update_many instead.
  upsert=upsert, **write_concern)
/Users/osteele/code/htl2/ABE/.direnv/python-3.6.5/lib/python3.6/site-packages/mongoengine/dereference.py:32: DeprecationWarning: generator 'QuerySet._iter_results' raised StopIteration
  items = [i for i in items]
/Users/osteele/code/htl2/ABE/abe/resource_models/label_resources.py:50: DeprecationWarning: generator 'QuerySet._iter_results' raised StopIteration
  return [mongo_to_dict(result) for result in results]

These are due to upstream issues in mongoengine:

• Stop using deprecated collection methods for PyMongo v3.x MongoEngine/mongoengine#1491
• Generator 'QuerySet._iter_results' raised StopIteration MongoEngine/mongoengine#1667