[Bioperl-l] DB::GenBank.pm etc. and net entrez queries

[chris.dag]

I was fooling around with scripts/bpfetch.pl and DB::GenBank.pm and saw 
that Entrez has changed the way they want HTTP post requests to be formatted:

Info page is at: 
http://www.ncbi.nlm.nih.gov:80/entrez/query/static/linking.html

The new base URL is supposed to be: 
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Command&db=Database&...

The base URL that we still use is (in DB::GenBank.pm at least):
http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?....

The Entrez people say the old format should still work and they have a 
utility called qmap.cgi that will map the "old" requests to the new URL.

The qmap cgi is at base URL:
http://www.ncbi.nlm.nih.gov/entrez/utils/qmap.cgi


Regarding our branch-06 that we are prepping for a 0.6.1 bugfix release:

o Do we do nothing since stuff appears to work still?
o Do we change the base URL to the remapper at qmap.cgi base (very easy to do)
o Do we change everything and use the new URL/command string structure?

To be polite at least if we are not going to use the new system we should 
at least be posting our HTTP to the remapping CGI. I just don't know if 
this falls under the category of "bug fixes only" for branch-06 since the 
current system seems to work ok.

Thoughts? I'm trying to dip slowly back into the code here :)

Also-- in our CVS head and bioperl-07 release are we going to take out the 
handcoded HTTP stuff and formally transition over to using the Net:: 
modules? At the very least that will get rid of the problems that 
behind-the-firewall people have been having since the libnet has good proxy 
code already.

-Chris