[DAS] Re: Bio::Das 0.59

[Lincoln Stein]

Hi Tony,

These all sound like reasonable fixes (I wonder why it works at all
for me?) If you have a chance, could you send me a patch file?
Or you could join the developer's group and do a CVS update.. up to
you.

Lincoln

Tony Cox writes:
 > On Thu, 29 Nov 2001, Lincoln Stein wrote:
 > 
 > 
 > Hi Lincoln, thanks for this. Next set of glitches I'm afraid:
 > 
 > In Request.pm the following always fails for me becasue $protocol only ever
 > contains the protocol number, not the full text string ("0.999" on my case).
 > 
 > #  my ($version) = $protocol =~ m!DAS/([\d.]+)! or
 > #    return $self->error('invalid X-Das-Version header');
 > 
 > I had to hack DASVERSION since dazzle only does 0.999 as yet I think.
 > 
 > #  $version >= DASVERSION or
 > #    return $self->error("DAS server is too old. Got $version; require at least
 > ${\DASVERSION}");
 > 
 > Having fixed/fudged this I then get:
 > 
 > Can't locate object method "toString" via package "Bio::Das::Feature" (perhaps
 > you forgot to load "Bio::Das::Feature"?) at /Bio/Das/Feature.pm line 169.
 > 
 > In Feature.pm we have:
 > 
 > sub toString {
 >   my $self = shift;
 >   return $self->label || $self->SUPER::toString;
 > }
 > 
 > but Feature no longer has a superclass so this fails. Changed this to:
 >   return $self->label || $self->id || ref($self);
 > 
 > after this is seems to work fine for me. I'll go try the proxy stuff now...
 > 
 > thanks
 > 
 > Tony
 > 
 > 
 > 
 > +>Hi Tony,
 > +>
 > +>The attached interim version of the Bio::Das module adds support for
 > +>proxies and hopefully also fixes the empty segment problems you were
 > +>experiencing (I couldn't reproduce the bug, but I fixed a suspicious
 > +>spot in the source).
 > +>
 > +>It's still not documented (sigh), but to turn on the proxy feature,
 > +>just call the Das object's proxy() method after creating it, and
 > +>before making any requests.  E.g.:
 > +>
 > +>  my $das = Bio::Das->new(15);  # timeout of 15 sec
 > +>  $das->proxy('http://kato.lsjs.org:80/');
 > +>
 > +>
 > +>
 > 
 > ******************************************************
 > Tony Cox			Email:avc@sanger.ac.uk
 > Sanger Institute		WWW:www.sanger.ac.uk
 > Wellcome Trust Genome Campus	Webmaster
 > Hinxton				Tel: +44 1223 834244
 > Cambs. CB10 1SA			Fax: +44 1223 494919
 > ******************************************************
 > 

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

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