[Bioperl-l] Bio::Biblio

[Allen Day]

Jan,

You might consider using the NCBI database via their 'eutils' service 
instead.  Have a look at Bio::DB::Biblio::eutils.  I find it's more 
reliable and that PubMed is more up-to-date and complete than that EBI 
server.

-Allen


On Wed, 5 Jan 2005, Marc Logghe wrote:

> Happy Newyear to you all !
> 
> Jan, there is nothing to worry about concerning your code.
> It is just that there are some electricity problems at the EBI which caused the soap server to be down for while.
> So, most of the soap services are currently unavailable.
> The original message you find on the Taverna mailing list:
> http://sourceforge.net/mailarchive/forum.php?thread_id=6274312&forum_id=35847
> 
> So, I guess there is nothing that you can do besides waiting ;-)
> 
> HTH,
> Marc
> 
> 
> -----Oorspronkelijk bericht-----
> Van: bioperl-l-bounces at portal.open-bio.org namens Jan Teune
> Verzonden: wo 5-1-2005 13:10
> Aan: bioperl-l at bioperl.org
> Onderwerp: [Bioperl-l] Bio::Biblio
>  
> Hello @ all,
> I'm writing a small script to fetch PubMed-Articles. Since two weeks 
> before Christmas, I have a problem to fetch Articles. Below is some Code 
> and the Error-Message:
> 
> #!/usr/bin/perl -w
> use Bio::Biblio;
> my $pmid = "15542139";
> my $biblio = new Bio::Biblio(
>                  -access    => 'soap',
>                  -location    => 'http://industry.ebi.ac.uk/soap/openBQS',
>                  -destroy_on_exit => '0',
>                  );
> my $citation = $biblio->get_by_id($pmid);
> print $citation;
> The Error-Message:
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: --- TRANSPORT ERROR ---
> 502 Proxy Error
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:328
> STACK: try{} block /usr/share/perl5/Bio/DB/Biblio/soap.pm:119
> STACK: SOAP::Lite::call /usr/share/perl5/SOAP/Lite.pm:3006
> STACK: try{} block /usr/share/perl5/SOAP/Lite.pm:2950
> STACK: Bio::DB::Biblio::soap::get_by_id 
> /usr/share/perl5/Bio/DB/Biblio/soap.pm:368
> STACK: ./bibliotest.pl:9
> -----------------------------------------------------------
> 
> I'm happy for any kind of help,
> 
> Jan  :-)
> 
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