[Bioperl-l] EUtilities policy change

Mark A. Jensen maj at fortinbras.us
Thu Jan 28 14:05:43 EST 2010

Thanks Chris-- 
The soap modules currently set tool to "SoapEUtilities(BioPerl)". 
I agree that a default email is a bad idea (tm) (unless maybe it's 
hilmar's...?). I'd say a warning on unset email parameters is a responsible
"there be dragons" sort of treatment.
----- Original Message ----- 
From: "Chris Fields" <cjfields at illinois.edu>
To: "BioPerl-l" <bioperl-l at lists.open-bio.org>
Cc: "Mark A. Jensen" <maj at fortinbras.us>
Sent: Thursday, January 28, 2010 2:00 PM
Subject: EUtilities policy change

> All,
> Per NCBI's recent change in eutils user policy (effective June 1):
> http://bioperl.org/pipermail/bioperl-l/2009-December/031698.html
> Both the tool and email parameters ('-tool', '-email') are now required
> when making requests.  Note this will significantly break all modules
> requiring remote access to eutils (Bio::DB::GenBank/GenPept, some Biblio
> and Taxonomy stuff as well, IIRC).  This also applies to web services
> (SOAP-based access).  Mark, not sure how this affects your SOAP-based
> modules.
> I have reconfigured Bio::DB::EUtilities to follow this policy; the
> default tool setting has been 'bioperl' and will remain that way.
> However, there has been no default email, therefore setting this is now
> required for future requests unless we (the bioperl devs) decide there
> is a safe default email to utilize.  My gut tells me, however, that
> falling back to a default email opens up a can of worms for the devs and
> is very likely a 'BAD IDEA'(TM).  
> Regardless, be aware that, after June 1, NCBI will very likely exclude
> requests with no email and will notify users who are considered to be
> violating their policies.
> I will likely make further changes to Bio::DB::EUtilities in the
> meantime to ensure that using the tools by default will not violate
> NCBI's policy (e.g. override this at your own risk).  
> chris

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