[Bioperl-l] EUtilities policy change

Mark A. Jensen maj at fortinbras.us
Thu Jan 28 14:55:31 EST 2010


Ok, SoapEU now warns on no email; passes email onto the fetch stage
during autofetch -- cheers MAJ
----- Original Message ----- 
From: "Chris Fields" <cjfields at illinois.edu>
To: "Mark A. Jensen" <maj at fortinbras.us>
Cc: "BioPerl-l" <bioperl-l at lists.open-bio.org>
Sent: Thursday, January 28, 2010 2:18 PM
Subject: Re: [Bioperl-l] EUtilities policy change


>I think warning is fine for now.  I've reimplemented that so it occurs
> lazily (warns only when a request is actually made).
> 
> Will also change the tool to 'BioPerl' (currently 'bioperl', all lc).
> We'll obviously have to address this in the test suite as well in some
> way, maybe ask for an email if network tests are requested.
> 
> chris 
> 
> On Thu, 2010-01-28 at 14:05 -0500, Mark A. Jensen wrote:
>> 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.
>> MAJ
>> ----- 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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