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

[Jessica Grant]

My problem was fixed by changing the db to "nuccore" and the rettype to "fasta".  Up until the other day, I was successfully using "nucleotide" and "gb".

Jessica







On Feb 17, 2012, at 9:41 AM, Peter Cock wrote:

> 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.
> 
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython