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jrderuiter / pybiomart

A simple pythonic interface to biomart.
MIT License
53 stars 11 forks source link

Parity in filter options with biomaRt #6

Open ivirshup opened 5 years ago

ivirshup commented 5 years ago

Increased available filters, should now have parity with biomaRt.

However, this seems to break a lot of the mocking tests, but I haven't quite figured out what to do about that. I'm not too familiar with mocking like this, and could use some pointers.

ivirshup commented 5 years ago

A little bit more on what I've done:

I've pretty much just translated some code from biomaRt for getting a list of filters, as biomaRt has many more available. The column name handling isn't pretty. As far as I can tell, that weird handling is for dealing with biomaRt archives 10 years ago. Since the oldest ensembl archive is from under 10 years ago this could no longer be relevant. That said, I haven't found documentation matching the call I'm making, so maybe there are other edge cases.

I didn't update setting attributes since there are more of them returned by get("configuration") than from get("attributes").

It might be possible to get filters out of the configuration, but it seems complicated, as there are >10000 options. In case filters are being missed, maybe the error for the filter or attribute not being found could be thrown only if the server rejects it?

coveralls commented 5 years ago

Coverage Status

Coverage increased (+0.4%) to 86.458% when pulling e64e62a1ff34afa081983eb899feb707c303bbec on ivirshup:more_filter_fields into 7802d45fe88549ab0512d6f37f815fc43b172b39 on jrderuiter:develop.

ivirshup commented 5 years ago

Ping @jrderuiter?