[Bioperl-l] EUtilities term handling

Sendu Bala bix at sendu.me.uk
Thu Oct 5 11:30:44 EDT 2006


Chris Fields wrote:
>>> I use URI for building the URL with the parameters.  URI specifically 
>>> encodes all of this for you, so spaces convert to '+' and '+' 
>>> converts to %2B.
>>
>> Well, yes. This causes what I thought of as a bug. It prevents me from 
>> submitting a /correct/ eutils term. However it isn't a bug if you 
>> explain to users they shouldn't be submitting valid eutils terms, but 
>> only valid /entrez/ terms.
> 
> I can specify in POD that URI encoding is in effect if that placates 
> you, and maybe add a bit about how terms are to be built (based on the 
> website).  I also noticed that the esearch POD doesn't have a demo in 
> the SYNOPSIS yet (my fault).
> 
> However, I think this is all a bit silly.  This is something most people 
> already realize and take for granted (it's standard for any CGI 
> interface to use URI encoding).
> 
> Also, most Entrez users do not use a term like 'BRCA2+Human[ORGANISM]'.  
> They use 'BRCA2 AND Human[ORGANISM]' or 'BRCA2 Human[ORGANISM]', the 
> latter which is implicit.  All of this is on the Entrez website.

Exactly. You're assuming an entrez user and expecting an entrez query. I 
don't think its silly given the name of the modules for the user to 
assume the code needs an eutils query, which is a different thing with 
different behaviour /independent/ of URI encoding.


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