[Biopython-dev] NCBI Abuse activity with Biopython

[Michiel de Hoon]

> > I would deprecate Bio.EUtils for another reason - there's no maintainer.
This is what I meant. I am sure that we can fix Bio.EUtils for now, but I don't see how we can maintain it in the future. That is why originally we decided to focus on Bio.WWW.NCBI (renamed to Bio.Entrez) instead.

> - although we are still using Bio.EUtils in Bio.GenBank
> (and probably in other places too).

As far as I can tell, Bio.GenBank is currently the only module in which Bio.EUtils is used, not counting modules that themselves have been deprecated. It shouldn't be too complicated to modify Bio.GenBank to use Bio.Entrez instead.

>>> 2) Remove the 'query' function from Bio.Entrez.
>>>  Anyway accessing NCBI's web site from Python
>>> to get HTML back doesn't make a lot of sense.
>
>> Okay, now I'm quite confused.  This is functionality
>> that Bio.EUtils supports.
>
> I think Michiel meant getting a handle containing
> raw HTML isn't very sensible, and this is what the
> Bio.Entrez.query() function does.  If it can only
> return HTML, then I agree, its not very useful and
> could be removed.
That is indeed what I meant. (It is still possible to get raw HTML by using the other EUtilities, for example efetch, but from a scripting language efetch is more likely to be used to get XML or some plain-text output).

--Michiel