Hi Seth, apologies for the delay, couldnt get back last week. I can see from your three XMLs, you have multiple set of exportables/importables between given two datasets. Could you please try setting default=1 and default=0 on your exportable (reporter_id_key). I would also drop multiple sets of exportables/importables for now, just for investigation, and keep this pair only (reporter_id_key). Export it and see the result.
Good luck! syed On Mon, 2007-06-11 at 17:22 +0100, seth redmond wrote: > On 11 Jun 2007, at 17:16, Syed Haider wrote: > > > Hi Seth, > > When you do saveAll, dont you get any template XML files for each of > > your xml files ? > > If so, please send me those as well > > > > Cheers > > Syed > > > > On Mon, 2007-06-11 at 17:06 +0100, seth redmond wrote: > >> marteditor 0.5, xmls attached. The exportable which isn't working is > >> the reporter_id_key from schema vb_map - looking at this now the > >> exportable appears correct, however there is something seriously wrong > >> with the tables and keys themselves. Where this springs from I don't > >> know... > >> > >> > >> -s > >> > >> > >> > >> > >> > >> On 11 Jun 2007, at 15:35, Syed Haider wrote: > >> > >>> Hi Seth > >>> could you please tell me which version of MartEditor you are using ? > >>> and could you send your XMLs please. > >>> > >>> Many thanks > >>> Syed > >>> > >>> > >>> On Mon, 2007-06-11 at 15:30 +0100, seth redmond wrote: > >>>> I keep getting the following message when linking two of my DBs, > >>>> either > >>>> directly or via a pointer filter: > >>>> > >>>>> ERROR: caught BioMart::Exception::Query: returning undef ... > >>>>> missing > >>>>> attributes for your exportable? > >>>>> > >>>>> Stacktrace: > >>>>> Exception::Class::Base::throw > >>>>> /home/snr02/work/biomart/0.5/biomart-perl/lib/BioMart/ > >>>>> ResultTable.pm: > >>>>> 140 > >>>>> BioMart::ResultTable::_new > >>>>> /home/snr02/work/biomart/0.5/biomart-perl/lib/BioMart/RootI.pm:42 > >>>>> BioMart::RootI::new > >>>>> /home/snr02/work/biomart/0.5/biomart-perl/lib/BioMart/DatasetI.pm: > >>>>> 1102 > >>>>> BioMart::DatasetI::getResultTable > >>>>> /home/snr02/work/biomart/0.5/biomart-perl/lib/BioMart/ > >>>>> QueryRunner.pm: > >>>>> 582 > >>>>> BioMart::QueryRunner::_processPath > >>>>> /home/snr02/work/biomart/0.5/biomart-perl/lib/BioMart/ > >>>>> QueryRunner.pm: > >>>>> 327 > >>>>> BioMart::QueryRunner::_getResultTable > >>>>> /home/snr02/work/biomart/0.5/biomart-perl/lib/BioMart/ > >>>>> QueryRunner.pm: > >>>>> 171 > >>>>> BioMart::QueryRunner::execute > >>>>> /home/snr02/work/biomart/0.5/biomart-perl/lib/BioMart/Web.pm:1848 > >>>>> (eval) > >>>>> /home/snr02/work/biomart/0.5/biomart-perl/lib/BioMart/Web.pm:1648 > >>>>> BioMart::Web::handle_request > >>>>> /home/snr02/work/biomart/0.5/biomart-perl/cgi-bin/martview:84 > >>>>> (eval) > >>>>> /home/snr02/work/biomart/0.5/biomart-perl/cgi-bin/martview:83 > >>>>> ModPerl::ROOT::ModPerl::Registry:: > >>>>> home_snr02_work_biomart_0_2e5_biomart_2dperl_cgi_2dbin_martview:: > >>>>> handler > >>>>> /usr/local/apache-2.0.55/lib/perl5/site_perl/5.8.8/x86_64-linux- > >>>>> thread-multi/ModPerl/RegistryCooker.pm:203 > >>>>> (eval) > >>>>> /usr/local/apache-2.0.55/lib/perl5/site_perl/5.8.8/x86_64-linux- > >>>>> thread-multi/ModPerl/RegistryCooker.pm:203 > >>>>> ModPerl::RegistryCooker::run > >>>>> /usr/local/apache-2.0.55/lib/perl5/site_perl/5.8.8/x86_64-linux- > >>>>> thread-multi/ModPerl/RegistryCooker.pm:169 > >>>>> ModPerl::RegistryCooker::default_handler > >>>>> /usr/local/apache-2.0.55/lib/perl5/site_perl/5.8.8/x86_64-linux- > >>>>> thread-multi/ModPerl/Registry.pm:30 > >>>>> ModPerl::Registry::handler -e:0 > >>>>> (eval) -e:0 > >>>> > >>>> The attribute it's looking for is there and I can query it within a > >>>> single dataset, it just doesn't seem to be loaded into the attribute > >>>> lists when used to link. > >>>> > >>>> Any suggestions? > >>>> > >>>> -s > >>>> > >>>> > >>> -- > >>> ====================================== > >>> Syed Haider. > >>> EMBL-European Bioinformatics Institute > >>> Wellcome Trust Genome Campus, Hinxton, > >>> Cambridge CB10 1SD, UK. > >>> ====================================== > >>> > > -- > > ====================================== > > Syed Haider. > > EMBL-European Bioinformatics Institute > > Wellcome Trust Genome Campus, Hinxton, > > Cambridge CB10 1SD, UK. > > ====================================== > > -- ====================================== Syed Haider. EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. ======================================
