Have you looked at SQLSoup ?  This library already does exactly what you're 
looking for.

https://sqlsoup.readthedocs.org/en/latest/


> For the most part, I have this working. However, the example in the gist 
> shows that:
> 
>     len(g.cpgIslandExt.all()) != g.cpgIslandExt.count()

What does your SQL echo output say?   Looking at the queries (and the rows 
returned, if you use echo='debug') will illustrate what's being sent.

A typical reason why all() returns fewer rows is when the query returns 
duplicate primary key identities - returned objects are uniqued on identity as 
they are received.   The fact that the "name" column is being hardcoded in your 
base model as the sole "primary key" for all mappings is the likely cause of 
this even being possible.   The reflection process already knows how to yield 
the primary key constraints defined on each table so you'd best rely upon that.






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