[Bioperl-l] Bio::DB::Taxonomy HTTPget query problem

[Aaron J Mackey]

The Bio::DB::Taxonomy::entrez interface is still experimental; a biosql
and taxonomy-dump flatfile interface is "coming soon".  Stay away.

But thanks for pointing out the missing functionality.

-Aaron

On Thu, 6 Mar 2003, Hilmar Lapp wrote:

> Bio::DB::Taxonomy provides a programmatic interface to NCBI's taxonomy
> server. Apparently it uses Bio::Root::HTTPget to make the http request.
>
> Here's the problem: if I run make test I get the following exception
> from Taxonomy.t:
>
> -------------------- WARNING ---------------------
> MSG: Can't query website:
> ------------- EXCEPTION  -------------
> MSG: request failed: HTTP/1.1 502 Proxy Error
> STACK Bio::Root::HTTPget::get blib/lib/Bio/Root/HTTPget.pm:155
> STACK (eval) blib/lib/Bio/DB/Taxonomy/entrez.pm:207
> STACK Bio::DB::Taxonomy::entrez::get_taxaid
> blib/lib/Bio/DB/Taxonomy/entrez.pm:206
> STACK toplevel t/Taxonomy.t:34
>
> --------------------------------------
>
> The first thing is I don't use a proxy and never have. Also, the 2
> preceding queries work fine, their tests pass. Knowing our friends from
> NCBI, I put in a sleep(10) before the last query - and voila, it works
> just fine. What's apparently happening is that queries get blocked if
> there are too many (more than 2) per time unit. This needs to be
> accounted for. I also don't know whether NCBI actually provides
> instructions about how to set up your own Taxonomy server. With Biosql
> the underpinning database is soon going to be there, but you'd still
> have to write the server.
>
> Apart from these considerations, there are actually 3 problems here:
>
> 1) The error message from HTTPget is confusing. I assume it is indeed
> the status line it gets from the HTTP server, so the problem would then
> lie there and not in HTTPget, and there's probably little we can do
> about it.
>
> 2) The line number in the stack trace is grossly wrong for HTTPget.
> Apparently the style of __PACKAGE__->throw instead of $self->throw
> yields wrong line numbers in the stack trace (maybe because comments
> are not counted?). Is there a specific reason for __PACKAGE__, or can
> it be replaced with $self? (ChrisD, Lincoln?)
>
> 3) Bio::DB::Taxonomy needs to adopt the delaying mechanism Lincoln
> implemented for the entrez query code.
>
> If no-one volunteers to take this on, I'll submit a bug report.
>
> 	-hilmar
>

-- 
 Aaron J Mackey
 Pearson Laboratory
 University of Virginia
 (434) 924-2821
 amackey at virginia.edu