[Biopython-dev] [BioPython] Fwd: NCBI Abuse Activity with BioPython

Peter biopython at maubp.freeserve.co.uk
Thu Jun 26 10:25:38 UTC 2008

Andrew wrote:
>  I thought I put a rate limiter into the code, but looking at it now I see I
> didn't.  The documentation clearly states that users must follow NCBI's
> recommendations, but who actually reads documentation?
>>> *  Send E-utilities requests to http://eutils.ncbi.nlm.nih.gov
>>> <http://eutils.ncbi.nlm.nih.gov/> , not the standard NCBI Web address.
> That change was announced on May 21, 2003, and most likely no one on the
> Biopython dev group tracks the EUtils mailing list.  It was also after I
> wrote the code, but to be fair I was subscribed to the utilities list at the
> time and should have caught the change.
> I think the correct fix is to this code in ThinClient.py:
>    def __init__(self,
>                 opener = None,
>                 tool = TOOL,
>                 email = EMAIL,
>                 baseurl = "http://www.ncbi.nlm.nih.gov/entrez/eutils/"):
> Change the baseurl to "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/".  I
> have not tested this.

I've tested that fix, and it seems to be OK with test_EUtils.py and
test_SeqIO_online.py which calls Bio.EUTils via Bio.GenBank, checked
in as Bio/EUtils/ThinClient.py revision 1.6

I'll have a look at your other specific suggestions too.  Thanks for
taking the time to go over this Andrew.


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