rm inter sample/prep tables and fixing tests

[antgonza]

Removing:

• study_sample_columns table
• prep_columns table
• type_loookup
• get_datatypes
• cast_to_python
• as_python_types
• convert_type

This also includes the code to transform all tables to varchar but is commented cause it increases the testing time dramatically.

[josenavas]

The only case that I'm concerned here is if there is a None in meta:

In [20]: l = [[1, 3], [None, 2]]

In [21]: df = pd.DataFrame(l, columns=['c1', 'c2'], dtype=str)

In [22]: df
Out[22]: 
    c1 c2
0    1  3
1  NaN  2

It changes the None to NaN. Can this case occur in here?

[antgonza]

I guess that's possible if something in the database is NULL but if it is, my guess is that it's fine ...

[josenavas]

I'm concerned about the warning at the end of this section on the pandas docs.

[antgonza]

Not sure what will be the solution to your concern ...

[josenavas]

Ideally, all NaNs should be Nones, but pandas for whatever reason it's applying some kind of transformation although you're passing dtype=str. I think the only option would be to force everything to be None afterwards using this:

In [32]: df
Out[32]: 
    c1 c2
0    1  3
1  NaN  2

In [33]: df.where(pd.notnull(df), None)
Out[33]: 
     c1 c2
0     1  3
1  None  2

[antgonza]

K

[josenavas]

👍

[coveralls]

Changes Unknown when pulling 35a7dee on antgonza:rm-inter-tables into * on biocore:str-ing_info_fles*.

[coveralls]

Changes Unknown when pulling 35a7dee on antgonza:rm-inter-tables into * on biocore:str-ing_info_fles*.

[antgonza]

@ElDeveloper, @wasade, @HannesHolste, do you guys have a (few) second(s) to review?

[josenavas]

👍 once test pass

[ElDeveloper]

👍 once tests pass.

[HannesHolste]

Looks good.

[coveralls]

Changes Unknown when pulling 8d9c655 on antgonza:rm-inter-tables into * on biocore:str-ing_info_fles*.