[Biopython] Bio/Entrez/efetch: Getting HTTP Error 500 Bio/Entrez/efetch: Getting HTTP Error 500 Bio/Entrez/efetch: Getting HTTP Error 500

[Peter Cock]

On Fri, Feb 17, 2012 at 1:36 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> On Fri, Feb 17, 2012 at 1:14 PM, Matej Repič <Matej.Repic at ki.si> wrote:
>> Fortunately, the fix is quite simple:
>>
>> Substitute the id=idlist in you fetch line with id=",".join(idlist).
>>
>
> Hi Matej,
>
> Well spotted. ...
>
> It is possible the NCBI may opt to "fix" this, but it looks like it was only
> working in the past by accident. However, we can do the conversion inside
> the Bio.Entrez.efetch function in future - we're due for another Biopython
> release now anyway so you shouldn't have to wait too long.
>
> I'm having general errors from the Entrez server right now - so I can't confirm
> the problem or test the potential fix yet.

I guess they kicked the server or something - it is working again now, and
I could confirm Matej Repič's findings and test my fix based on them:
https://github.com/biopython/biopython/commit/01b091cd4679b58d7e478734324528dd9d52f3ed

If anyone needs the fix right now, you must install Biopython from source,
or at least update the Bio/Entrez/__init__.py file by hand. Some testing
would be appreciated - and then we'll try to expedite the release of
Biopython 1.59 by the end of the month.

Peter

P.S. If anyone wants a small challenge for contributing to Biopython, an
online unit test for this and other things in Bio.Entrez would be great.
Please ask for more information on the biopython-dev list if you're
interested in helping out.