[Bioperl-l] Eutilities epost/efetch problem

[Kristine Briedis]

Hi Chris,

I'm not getting the error anymore.  NCBI must have fixed something.

Cheers,
Kristine


-----Original Message-----
From: Chris Fields [mailto:cjfields at illinois.edu] 
Sent: Tuesday, May 12, 2009 11:36 AM
To: Kristine Briedis
Cc: Warren Gallin; BioPerl List
Subject: Re: [Bioperl-l] Eutilities epost/efetch problem

Not showing up in tests, so this may be something very specific that  
changed.  I'll try to reproduce it.

chris

On May 12, 2009, at 12:19 PM, Kristine Briedis wrote:

> Hi Warren,
>
> We've noticed the same EFetch error.  I emailed NCBI and will let  
> you know what they say.
>
> Cheers,
> Kristine
>
>
> ===============================
> Kristine Briedis, Ph.D.
> Bioinformatics Software Engineer
> Accelrys, Inc.
> 10188 Telesis Court, Suite 100
> San Diego, CA 92121  USA
> kbriedis at accelrys.com
>
>
>
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org 
> ] On Behalf Of Warren Gallin
> Sent: Monday, May 11, 2009 6:36 PM
> To: BioPerl List
> Subject: [Bioperl-l] Eutilities epost/efetch problem
>
> Hi folks,
>
> 	Something started failing for me this morning that had been working  
> reliably for the last week,
>
> 	I post an array of gi numbers, a history is successfully returned,  
> but when I try to use efetch to get the records, it fails with the
> error:
>
>
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: Response Error
> Not Found
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /Library/Perl/5.8.8/Bio/Root/Root.pm:368
> STACK: Bio::DB::GenericWebAgent::get_Response /Library/Perl/5.8.8/Bio/
> DB/GenericWebAgent.pm:215
> STACK: 090507_Stable_gb_update.pl:238
> -----------------------------------------------------------
>
>
> 	I'm running the efetch inside an eval and letting it try a total of 6
> times with a 5 sedond sleep in between, but the error is consistent.
>
> 	So I consider two possibilities:
> 	1) Has something changed on the Entrez server recently?  Has anyone
> else started having this kind of problem?
>
> 	2) Have I inserted some subtle flaw into my code that would lead to a
> failure of efetch.
>
> 	I am attaching two text files, one with the code chunklet that is
> doing this and the other the output from the script.
>
> 	Any help or suggestions are profoundly appreciated.
>
> Warren Gallin
>
>
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