Resolve pylint errors

[lhuhmann]

Resolving pylint errors will make the code more generally usable (including in the form of a package, which @brendanreardon recently made an issue for). To see which errors exist, run pylint --disable=all --enable=E.

[lhuhmann]

I'm happy to take on this issue!

[lhuhmann]

I was able to resolve most of the errors, but there are some remaining errors where things seemed to be used but not defined:
(1) In multiple places the code seems to look for CONFIG, but this doesn't seem to be defined anywhere.
(2) In a few places, Datasources.generate_db_dict() is used, but this doesn't seem to be defined anywhere.
(3) In one place, Preclinical.import_dbs() is called, but a required argument, paths_dictionary, is not supplied.

Below I've included the full screenshot of the error check output (there are more than three errors, but I believe at this point the remaining errors are all one of the three above problems), which was generated using pylint --disable=all --enable=E.

I'm hoping maybe @brendanreardon can help me with either information needed to fix these errors, or letting me know that some of this code can be deleted if we are no longer care about it (and that's why it's broken).

[brendanreardon]

Hi @lhuhmann, thanks for taking a look at this. We are not going to be moving forward with this change at this time, maybe in the future. Changing the import structure results in circular imports with how this repository is currently structured, and thus how it is being used by implementations. Moving forward with this would result in breaking changes. This version is essentially written as an executable, see our execution instructions for current intended usage.

Regarding the internal import structure, these are functions within classes of other modules in the codebase. Last year, we refactored the codebase to remove CONFIG as a global variable, with Paul at the VA, but removing the column names config would result in a huge rewrite so it is low on our priority.