[Bioperl-l] EUtilities term handling

Chris Fields cjfields at uiuc.edu
Thu Oct 5 12:12:11 EDT 2006


On Oct 5, 2006, at 11:02 AM, Sendu Bala wrote:

> Chris Fields wrote:
>>
>>>>     * Correct: &term=biomol+mrna[properties]+AND+mouse[organism]
>>>
>>> The correct query is the one that has +s in it.
>> Yes, that's because it's a URL, not a raw search term string (it  
>> has been URI-encoded so spaces are converted to '+').  If you use  
>> that as a direct query in Entrez you will not get the same response.
>
> But we're not doing Entrez queries. We're using a module called  
> EUtilities to do an eutils query, which involves forming a url in  
> which spaces should to be converted to +. That's the source of  
> confusion. Is the user supposed to do this, or is EUtilities?
>
> All you had to do 8 emails ago is tell me that EUtilities is  
> supposed to do that. You /still/ haven't told me that. I give up.

It should be apparent from the documentation and the URLs posted in  
debugging output the first few times you used it.  Again, why would I  
dedicate ~ 10 classes to pasting together URI-encoded strings?

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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