[Biojava-l] Re: Experimental DAS 1.900 implementation / biodas code on our servers

[Lincoln Stein]

Thanks Chris, 

I'm hoping the WashU DNS admins will have an ETA for me today.

Lincoln

chris dagdigian writes:
 > 
 > 
 > Thanks for clarifying that Jason!
 > 
 > Jason is dead right. A long time ago we decided for security reasons 
 > (nobody trusts cvs pserver that much..) that all anonymous cvs access 
 > would have to be via a standalone box. Hence the cvs.bio{whatever}.org 
 > hostnames.
 > 
 > Regarding getting Biodas.org sorted -- I've done as much as I can with 
 > GID/account creation, apache vhosts and whatnot. Lincoln has already 
 > started cvs init'ing codebase repositories. I'm waiting now for the DNS 
 > stuff to happen. I can't really set up mailing lists, cvs.biodas.org or 
 > even the web cvs stuff without working DNS...well actually I could set 
 > them up but it would not be all that useful :) I understand via Lincoln 
 > that DNS changes are in progres.
 > 
 > Regards,
 > Chris
 > 
 > 
 > 
 > Jason Stajich wrote:
 > 
 > > For clarification.
 > > 
 > > cvs.bio{*}.org is a replication of bio{*}.org not the same machine.  We
 > > rsync the cvs repositories on cvs.bio{*} from bio{*} machine every 2
 > > hours.
 > > 
 > > So:
 > > cvs.biodas.org is where anonymous cvs will live, devs who need write
 > > access to the das cvs repository will need accounts on the biodas.org,
 > > those just checking out anonymous versions can obtain via cvs.biodas.org
 > > or through webcvs for browsing.  see http://cvs.bioperl.org.
 > > 
 > > (Chris can you make sure Lincoln's new biodas repositories
 > >  are added to the rsync list when you setup webcvs)
 > > 
 > > * = (perl|java|python|corba|xml|das) 
 > > 
 > > On Tue, 12 Jun 2001, Lincoln Stein wrote:
 > > 
 > > 
 > >>Hi Thomas, et al.,
 > >>
 > >>I've moved the biodas repository to cvs.biodas.org (physically the
 > >>same machine as biojava.org, I think).  Shall we move the CVS
 > >>repository there and integrate the biodas.org and biojava.org/das web
 > >>pages? (I'll do the stitching together).
 > >>
 > >>Lincoln
 > >>
 > >>Thomas Down writes:
 > >> > Hi...
 > >> > 
 > >> > I've started working on an experimental Java implementation of
 > >> > the DAS 1.900 proposal, so that we've got something to play
 > >> > with as the specification develops.  At the moment there's
 > >> > just a Sequence service (vaguely equivalent to refererence
 > >> > servers in DAS1).  I've got most of the pieces of a Features
 > >> > service, and should be able to check that in in the next day
 > >> > or so.
 > >> > 
 > >> > For anyone who's interested in tracking development, there's
 > >> > code in the BioJava CVS repository (http://cvs.biojava.org/
 > >> > for more info).  Checkout the module `xdas'.
 > >> > 
 > >> > What you get:
 > >> > 
 > >> >   - Prototype DAS sequence service
 > >> > 
 > >> >   - The SOAP toolkit it relies on.
 > >> > 
 > >> >   - An obligatory stock-quote demo ;)
 > >> > 
 > >> > To preempt the inevitable question, yes I have looked at other
 > >> > SOAP toolkits (especially the IBM/Apache one).  While they're good
 > >> > a lot of the time, they tend to use DOM to represent the SOAP messages
 > >> > in-memory.  I know from past experience that this really isn't a good
 > >> > idea where DAS is concerned -- sometimes you want to shift quite
 > >> > serious amounts of data around (especially feature-tables), and I've
 > >> > seen OutOfMemoryErrors (as well as poor performance) when the BioJava
 > >> > DAS client was using a DOM based solution.
 > >> > 
 > >> > The new SOAP toolkit is based on S[t]AX event-based XML parsing,
 > >> > so that should help scalability.
 > >> > 
 > >> > 
 > >> > I'd be interested to hear any comments about this code...
 > >> > 
 > >> > 
 > >> >    Thomas.
 > >>
 > 
 > > 
 > 
 > 

-- 
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Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein@cshl.org			                  Cold Spring Harbor, NY

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