[Biopython] [BioPython] Question about using Entrez.epost

[Peter]

On Thu, May 7, 2009 at 9:59 AM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> I think I see what is going on now.  Using an HTTP POST would avoid
> long URL problems with an HTTP GET (something the NCBI documents
> don't explain - at first reading the EPost command seems redundant).
> However,  from looking over our Bio.Entrez code more carefully it
> seems we are not actually using a POST after all - just a plain HTTP
> GET.
>
> This would explain the limit you are seeing - you are either the first
> person to try such a long ID list with Bio.Entrez (personally I have
> only ever downloaded much smaller datasets in one go), or at least
> you are the first person to actually report it is broken.  So thank you!
>
> I've filed Bug 2824 on this issue:
> http://bugzilla.open-bio.org/show_bug.cgi?id=2824

Fixed in CVS (which will propagate to github shortly).  All you need to do
to apply the fix is update your .../site-packages/Bio/Entrez/__init__.py file
with the new version, which can be downloaded from here shortly:

http://cvs.biopython.org/cgi-bin/viewcvs/viewcvs.cgi/biopython/Bio/Entrez/__init__.py?cvsroot=biopython

Or, just install all of Biopython from the latest source (fetched from CVS
or github).  If you need more details instructions, let us know.

This should fix your EPost problem - if you can confirm this by email
that would be great.

Thank you.

Peter