Refactor code to use metadata endpoints

[hesspnnl]

There is no difference between the between the Find enpoints /{collection}/ and Metadata nmdc/{collection_name}. They are reaching into the same data source. Katherine recommends I should only use the nmdc/{collection_name} endpoint and create the mongo filters for the things ie by pi, id, name, etc.
If the user wants to then can pass in more filters.

[hesspnnl]

began this change in the biosample class. will bring this to study as well.