[Open-bio-l] Toolkits and the new eutils policies

[Chris Fields]

On Mar 25, 2010, at 5:39 PM, Peter wrote:

> On Thu, Mar 25, 2010 at 7:59 PM, Ewan Birney <birney at ebi.ac.uk> wrote:
>> 
>> On Thu, 25 Mar 2010, Peter wrote:
>>> 
>>> Thanks Chris (& Eric),
>>> 
>>> Looks like we are fine as things stand: continue to
>>> encourage the user to set the email (with a warning
>>> if omitted), and try to encourage them to override the
>>> tool parameter if appropriate (e.g. if part of a larger
>>> application like a Galaxy workflow).
>>> 
>>> [I don't see any point in forcing people to invent
>>> tool names for each of their one off Entrez scripts,
>>> or interactive sessions - defaulting to BioPerl etc
>>> here seems sane]
>> 
>> At the very least teh default should be "BioPerl Toolkit Placeholder For Non
>> Registered Client" so that NCBI know precisely that the end programmer has
>> not put something in there sensibly.
> 
> No, that's just silly IMHO. Using "BioPerl" on its own serves just
> the same purpose (indeed, the NCBI will be used to this from
> existing users and all versions of BioPerl to date), The extra
> long version doesn't add any useful information and more
> importantly makes the URLs much longer which can be a
> real issue because long URLs can break (e.g. if going via
> a proxy).


I don't think this is meant literally, just the general idea that setting it to a specific value indicates the user in question didn't reset it.


>> And there should be a loud warning. I think it's fine to actually
>> throw an exception. If someone is running a one off script, then they
>> made the function call and can modify it. If someone's developing something
>> more serious then they've got the time to think it through.
>> 
>> I see little benefit in letting a default happen with just a warning.
> 
> Making the email and/or tool mandatory vs throwing an
> exception just an implementation detail.
> 
> I think the issue is should BioPerl etc treat the email and
> tool as optional, optional with a warning, or mandatory.
> Note the NCBI does not seem to be making them
> mandatory (for now).
> 
> Peter


It is listed as a user requirement here, has been for a long while actually:

http://www.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html#UserSystemRequirements 

It just hasn't been enforced.  The new rule, as I understand it, is they will likely start enforcing it.

chris