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

Tue Jan 21 13:02:12 EST 2003

thank for your answers,

i didn't touch anything in code and it works again,
so i think it was a temporary server problem.

Damien

Jason Stajich wrote:
> 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
> 

-- 
----------------------------
Damien Mattei
C.N.R.S / U.N.S.A - UMR 6549
mailto:mattei@unice.fr
http://www-iag.unice.fr/
----------------------------