Hi Simon,
presume you are on codebase 0_4?
from the martview line it looks like it fails when trying to add an
attribute as below which should not be possible as it tests whether $entry
is defined. Is your code fully up to date - could be that we added some of
the catching code as a bug fix.
This code is all for ADF output - presume your interface works fine if you
are using another format type?
my $entry =
$REGISTRY->getDatasetByName($CGI->param('schema'),$\dataset)->
getConfigurationTree->getAttributeByName($_);
next if (!$entry);
$query->addAttribute($entry) if ($entry);
Best wishes
Damian
On Wed, 2 Aug 2006, Twigger Simon wrote:
> Hi there,
>
> I'm working on a mart and all was well but something happened (not
> sure what I did) and now I'm having trouble exporting from the mart.
> Filtering works fine but when I come to export the final results I
> get an error on screen and this error listed in the server error_log:
>
> -------------------- EXCEPTION --------------------
> DATE: 2-AUG-2006
> MSG: Tried to add nonexistent attribute to query
> STACK BioMart::Query::addAttribute /project/biomart/biomart-web/
> biomart-plib/BioMart/Query.pm:691
> STACK martview::initialise_results /project/biomart/biomart-web/perl/
> multi/martview:3433
> STACK martview::print_results /project/biomart/biomart-web/perl/multi/
> martview:2853
> STACK Apache::ROOT::perl::biomart::martview::handler /project/biomart/
> biomart-web/perl/multi/martview:185
> STACK (eval) /usr/local/lib/perl5/site_perl/5.8.7/sun4-solaris/Apache/
> Registry.pm:149
> STACK Apache::Registry::handler /usr/local/lib/perl5/site_perl/5.8.7/
> sun4-solaris/Apache/Registry.pm:149
> STACK (eval) /dev/null:0
> STACK toplevel /dev/null:0
> -------------------------------------------
>
> [Wed Aug 2 11:01:09 2006] [error] at /project/biomart/biomart-web/
> perl/multi/martview line 3433\n
>
> I've checked all the attributes in marteditor and they look OK, Ive
> use the validate menu option in mart editor and I dont get any errors
> (this opens up a new marteditor window with a few new attributes that
> its noticed that I havent added but I dont get any error messages).
> I've exported the (presumably) validated configuration back to the
> mart and restarted the server and still get the same error. All my
> other marts work fine so somehow this one configuration is having
> trouble.
>
> Anyone suggest how I might find out more about what is going wrong so
> I can fix it - what nonexistent attribute its trying to add, etc.?
>
> Cheers,
>
> Simon.
>
> --
>
> Simon N. Twigger, Ph.D.
> Assistant Professor, Department of Physiology
> Medical College of Wisconsin
> 8701 Watertown Plank Road,
> Milwaukee, WI, USA
> tel: 414-456-8802
> fax: 414-456-6595
> AIM/iChat: simontatmcw
>
>
>
