[DAS] LDAS/DasClient problems

[Brian Gilman]

Sounds good to us. We'll be releasing a new version of omniview on Feb
21st which will be up to date with the spec. 


				-B

-----------------------
Brian Gilman <gilmanb@genome.wi.mit.edu>
Sr. Software Engineer MIT/Whitehead Inst. Center for Genome Research
One Kendall Square, Bldg. 300 / Cambridge, MA 02139-1561 USA
phone +1 617  252 1069 / fax +1 617 252 1902


On Wed, 6 Feb 2002, Lincoln Stein wrote:

> I'm making the changes to LDAS first (to make sure I'm happy with them), and 
> then I'll release new DTDs and a spec.  But I'll be releasing the DTDs first 
> so that you have plenty of time to make the omnidas changes (and ditto for 
> Dazzle and Bio::DAS) before releasing the new LDAS.
> 
> Does this sound OK?
> 
> Lincoln
> 
> On Tuesday 05 February 2002 18:51, Brian Gilman wrote:
> > Hello all,
> >
> >
> > 	Do we have a new DTD for this spec?? It looks like our client will
> > not be able to connect to any new LDAS backended server with the new
> > changes in place. I'm thinking of good ideas ways of being able to connect
> > to any DAS server but I'm finding myself in spec hell right now.
> >
> > 	Here's the current thoughts:
> >
> > 	1) Look at HTTP header for das version
> > 	2) Get instance of builder object for the XML handler instances
> > 	3) Stream XML into this handler
> > 	4) Pass objects to client
> >
> >
> > 	We use a validating parser on the backend to make sure the data
> > coming down the wire is valid. This is the reason our group keeps finding
> > little niggly bugs in the servers different groups have implemented.
> > Hopefully we can keep people "true" to the spec. Anyway, suggestions are
> > welcome as to how to do this sort of thing.
> >
> > 				Best,
> >
> > 					-B
> >
> > -----------------------
> > Brian Gilman <gilmanb@genome.wi.mit.edu>
> > Sr. Software Engineer MIT/Whitehead Inst. Center for Genome Research
> > One Kendall Square, Bldg. 300 / Cambridge, MA 02139-1561 USA
> > phone +1 617  252 1069 / fax +1 617 252 1902
> >
> > On Tue, 5 Feb 2002, Thomas Down wrote:
> > > On Fri, Feb 01, 2002 at 04:06:57PM -0800, Mr Dmitriy Ryaboy wrote:
> > > > Hi everyone,
> > > > I've been trying to set up a DAS annotation server at
> > > > http://zilla.lbl.gov/cgi-bin/das , but I keep running
> > > > into some problems..  I installed LDAS following
> > > > Lincoln Stein's excellent instructions, and using
> > > > slightly different test data (see below, along with
> > > > the .conf file).  Ldasdump works, http query work.
> > > > When I try to view the annotation on Ensembl's
> > > > DasClient, however, I get the following error:
> > >
> > > Hi...
> > >
> > > I've added a workaround to the BioJava DAS library which
> > > now allows it to communicate with the current LDAS release.  You can
> > > download a new DasClient build including this code from:
> > >
> > >    http://www.biojava.org/download/das-client/
> > >
> > > (Make sure you get the latest build -- currently 20020205).
> > >
> > > There are still a couple of other issues:
> > >
> > >   - When the client requests a stylesheet from your server,
> > >     the HTTP connection gets dropped (without even an error
> > >     message).  This suggests some kind of server error -- not
> > >     sure if this is an LDAS bug or a local misconfiguration.
> > >     You'll get an error as a result of this, but if you click
> > >     `Continue', DasClient will auto-generate a stylesheet then
> > >     carry on, so don't worry about it too much for now.
> > >
> > >   - Having connected to your server, I can browse around
> > >     without any errors, but I must confess that I haven't
> > >     actually seen any features.  This might just mean that
> > >     there aren't very many features in your server and I
> > >     haven't looked in the right place, but it could also mean
> > >     there's a problem -- especially if, as you say, you can't
> > >     see features on the Ensembl website either.
> > >
> > >
> > > Let me know if I can help any further with this,
> > >
> > >     Thomas.
> > > _______________________________________________
> > > DAS mailing list
> > > DAS@biodas.org
> > > http://biodas.org/mailman/listinfo/das
> >
> > _______________________________________________
> > DAS mailing list
> > DAS@biodas.org
> > http://biodas.org/mailman/listinfo/das
> 
> -- 
> ========================================================================
> Lincoln D. Stein                           Cold Spring Harbor Laboratory
> lstein@cshl.org			                  Cold Spring Harbor, NY
> ========================================================================
>