[Bioperl-l] Eutilities epost/efetch problem

[Chris Fields]

Same here (no error).  Just ran the below.

chris

#!/usr/bin/perl -w

use strict;
use warnings;
use Bio::DB::EUtilities;

my @gi_number = qw(
41395563
31618162
81831839
54038971
);

my $gpeptfactory = Bio::DB::EUtilities->new(
         -eutil          => 'epost',
         -db             => 'protein',
         -rettype        => 'gp',
         -retmode        => 'text',
         -tool           => 'VKCDB_Update',
         -email          => 'wgallin at ualberta.ca',
         -id             => \@gi_number,
         -keep_histories => 1);

my $hist = $gpeptfactory->next_cookie || die "Arghh!";

$gpeptfactory->set_parameters(-eutil => 'efetch',
                               -history => $hist);

$gpeptfactory->get_Response(-file => '>test.gb');

On May 12, 2009, at 1:42 PM, Kristine Briedis wrote:

> 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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>