[Bioperl-l] XEMBL deprecation

Lincoln Stein lstein at cshl.edu
Fri Feb 16 08:55:06 EST 2007


I like the idea of converting these over to use DBFetch's SOAP services. On
the other hand, it isn't llikely that I'm going to have time to do this
anytime soon.

Probably the best thing to do is to issue a warning and return undef if
someone tries to use othe XEMBL module. I'll make that change.

Lincoln

On 2/15/07, Chris Fields <cjfields at uiuc.edu> wrote:
>
> I have gone ahead and marked Bio::DB::XEMBL and Bio::DB::XEMBLService
> both for deprecation in the wiki and in CVS (though I haven't set any
> timeline):
>
> http://www.bioperl.org/wiki/Deprecated_modules
>
> The XEMBL web services are no longer available, and it looks like
> everything is running through DBFetch now.  The XEMBL tests are
> skipped if no server is detected, so they shouldn't cause any
> problems with Bioperl installations.
>
> Lincoln, was there anything to salvage from these?  I noticed they
> used SOAP::Lite, so maybe we could convert these over to a SOAP-based
> interface to DBFetch web services?
>
> chris
>



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Lincoln D. Stein
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