[DAS] Re: Bio::Das 0.59

[Tony Cox]

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/');
+>
+>
+>

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