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

[Ewan Birney]

On Sat, 23 Sep 2000, chris.dag wrote:

> 
> 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 :)


I think teh best thing is to move the URL over but not change any parsing
code if that is possible.

> 
> 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.

I guess we should do all http: through "standard" perl modules, so, yes,
for main trunk make the change...


> 
> -Chris
> 
> 
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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
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