[Bioperl-l] Bio::DB::GenBank and proxy

[William Kenworthy]

Unfortunately, this didn't work for me:

declare -x http_proxy="http://localhost:8081"
wdk at rattus tmp $ ./t.pl
Attempt to bless into a reference at
/usr/lib/perl5/site_perl/5.8.0/LWP/UserAgent.pm line 221.
wdk at rattus tmp $ 

Noticed another thing: the cache (squid in my case) always reports a
"miss", and fetches direct.  Not sure why this is the case - would be
handy as we have students with a tight network allowance that would
benefit from cacheing - as it is, this looks like an assignment (cache
the data you fetch ...).  

This is what ethereal shows as "on the wire" after the second try etc
requests:

GET
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?retmode=text&rettype=gb&db=nucleotide&tool=bioperl&id=gb%7CAL022723&usehistory=n HTTP/1.1
TE: deflate,gzip;q=0.3
Connection: TE, close
Host: eutils.ncbi.nlm.nih.gov
User-Agent: Bio::DB::GenBank/0.8

HTTP/1.0 200 OK
Date: Tue, 12 Aug 2003 11:16:14 GMT
Server: Apache
Content-Type: text/plain
Via: 1.1 eutils.ncbi.nih.gov
X-Cache: MISS from eutils.ncbi.nih.gov
X-Cache: MISS from rattus.Localdomain
X-Cache-Lookup: MISS from rattus.Localdomain:8081
Proxy-Connection: close

LOCUS  ...

Wont add this to the bugzilla for awhile in case someone wants to
comment.

BillK


On Tue, 2003-08-12 at 15:53, simon andrews (BI) wrote:
> > -----Original Message-----
> > From: William Kenworthy [mailto:billk at iinet.net.au]
> > Sent: 10 August 2003 23:43
> > To: BioPerl List
> > Subject: [Bioperl-l] Bio::DB::GenBank and proxy
> > 
> > 
> > Hi, is there a way to get Bio::DB::GenBank to honour a local 
> > proxy from the environment (i.e., HTTP_PROXY or similar), or 
> > does it have to be implicitly specified via 
> > "$db->proxy(['http','ftp'], 'http://proxy:8081' );"
> 
> I've just filed a bug report which turns on this behaviour in
> the BioPerl modules which require internet access.  Take a
> look at:
> 
> http://bugzilla.bioperl.org/show_bug.cgi?id=1482
> 
> ...two quick changes to core modules and you're good to go.
> 
> I've also just noticed that there's a typo in the report.
> The second module should be Bio::DB::Query::WebQuery.pm
> 
> Hope this helps
> 
> Simon.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
-- 
William Kenworthy <billk at iinet.net.au>