[Potential bug] Inconsistent query() input for MongoDbDatabase and TinyDbJson

[hlmore]

Beaverdam originally handled only MongoDB as a database backend, so MongoDbDatabase.query() was designed to correspond nicely to the pymongo's .find() function. Since then, TinyDB has also been added as a possible database backend, but because its .search() function has a different structure, TinyDbJson.query() has slightly different input.

At the moment, this results in some slightly un-beautiful code where MongoDbDatabase.query() accepts either a dict, strings, or a list of strings as query_output, and TinyDbJson.query() only accepts a string or list of strings.

In practice, this isn't currently a concern, because we aren't using any of the more advanced output functions.

In future, to handle more complex queries, a unified set of inputs to MetadataSource.query() should be chosen, and then these inputs should be appropriately parsed in the subclass functions MongoDbDatabase.query() and TinyDbJson.query() (and whichever other backends will be used).