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

[Alexandra Schnoes]

Wow. That was quick! Thanks guys!
Alex

On Fri, Feb 17, 2012 at 6:52 AM, Jessica Grant <jgrant at smith.edu> wrote:

> 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.
> >
> > _______________________________________________
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>
>
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