[Bioperl-l] Can't connect to www.ncbi.nih.gov:80 (Bad hostname'www.ncbi.nih.gov')

Mon Jan 20 14:00:43 EST 2003

Actually that IP should have been okay.

bioperl 1.2 uses the same URL so the upgrade won't get you that (although
the upgrade will get you access to more Entrez features).

I'll change things back to the full IP just in case but I think the
problem relates to the ftp server (ftp.ncbi.nih.gov) not responding which
maybe was relaying port 80 requests to the webserver.

You can workaround the problem by using the following to change the base
URL for the requests until things resolve themselves.

use Bio::DB::GenBank;
use Bio::DB::NCBIHelper;

$Bio::DB::NCBIHelper::HOSTBASE = 'http://www.ncbi.nlm.nih.gov';

my $db= new Bio::DB::GenBank();

---
I think there was confusion because NCBI requested that FTP traffic be
addressed ftp.ncbi.nih.gov that the whole domain was moving up.

For the record, the following works for me and all the tests worked fine
for me on 1.2 which used that addr.

jason@babelfish $ telnet www.ncbi.nih.gov 80
Trying 130.14.29.110...
Connected to www.ncbi.nih.gov.
Escape character is '^]'.
GET /
<html>
<head>
<title>NCBI HomePage</title>
...
[cut]

On Mon, 20 Jan 2003, Francis Ouellette wrote:

>
> Dear Damien,
>
> That domain name should have never worked!
>
> wrong:     www.ncbi.nih.gov
>
> correct:   www.ncbi.nlm.nih.gov
>                     ^^^
> cheers,
>
> f.
>
>
>
>
> Damien Mattei wrote:
> >
> > i wrote some code last year which worked well, and didn't run during 1
> > or 2 months,now i get an error:
> >
> > $seq = $dbn->get_Seq_by_acc($bacname); # this returns a Seq object
> >
> > The code threw this exception
> >
> > ------------- EXCEPTION  -------------
> > MSG: WebDBSeqI Request Error:
> > 500 (Internal Server Error) Can't connect to www.ncbi.nih.gov:80 (Bad
> > hostname 'www.ncbi.nih.gov')
> >
> > i'm using  bioperl-1.1.1 from CVS (29 oct 2002), should i upgrade again
> > or is it a problem on the NCBI servers.
> >
> > thanks to help
> >
> > Damien
> > ----------------------------
> > Damien Mattei
> > C.N.R.S / U.N.S.A - UMR 6549
> > mailto:mattei@unice.fr
> > http://www-iag.unice.fr/
> > ----------------------------
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
>
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu