[Bioperl-l] Eutilities epost/efetch problem

[Chris Fields]

Rob,

The error message is generated on their side or from LWP; from  
GenericWebAgent:

         if ($response->is_error) {
             $self->throw("Response Error\n".$response->message);
         }

We could change that, but I try to leave it as generic as possible.

chris

On May 12, 2009, at 2:19 PM, Robert Buels wrote:

> I don't think this is terribly unusual to have Efetch go down.  I  
> have an automated pipeline that uses efetch to cross-check some  
> stuff, and it goes down every once in a while, sometimes for up to a  
> day or so.
>
> Might consider having a little nicer error message for this case?
>
> Rob
>
> -- 
> Robert Buels
> Bioinformatics Analyst, Sol Genomics Network
> Boyce Thompson Institute for Plant Research
> Tower Rd
> Ithaca, NY  14853
> Tel: 503-889-8539
> rmb32 at cornell.edu
> http://www.sgn.cornell.edu
>
>
>
> Chris Fields wrote:
>> 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
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>
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