[Bioperl-l] EUtilities term handling

Sendu Bala bix at sendu.me.uk
Thu Oct 5 12:28:51 EDT 2006


Chris Fields wrote:
> 
> 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?

I'm not sure how not doing URI-encoding would suddenly make your classes 
worthless. I find them to be very useful (even when I didn't know there 
was any URI-encoding, was incorrectly using +s and it happened to work 
anyway).


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