Hello Michael, There was an error in the query. Please note the amendment: <Filter name = "with_variation_annotation" excluded = "0"/>
Also please change the link to martservice in the webExample.pl file to read like this: my $path="http://www.ensembl.org/biomart/martservice?";; Regards, Jorge. On Tue, 2010-03-09 at 15:54 +0100, Michael Dondrup wrote: > Hi I hope this is the right place to send BioMart Martview error reports, if > not please help anyway. > > I am trying to perform the following query (as xml export) which worked > earlier in BioMart/Martview: > <?xml version="1.0" encoding="UTF-8"?> > <!DOCTYPE Query> > <Query virtualSchemaName = "default" formatter = "TSV" header = "0" > uniqueRows = "0" count = "" datasetConfigVersion = "0.6" > > > <Dataset name = "hsapiens_snp" interface = "default" > > <Filter name = "snp_source" value = > "with_variation_annotation"/> > <Attribute name = "refsnp_id" /> > <Attribute name = "chr_name" /> > <Attribute name = "chrom_start" /> > </Dataset> > </Query> > > URL: > http://www.biomart.org/biomart/martview?VIRTUALSCHEMANAME=default&ATTRIBUTES=hsapiens_snp.default.snp.refsnp_id|hsapiens_snp.default.snp.chr_name|hsapiens_snp.default.snp.chrom_start&FILTERS=hsapiens_snp.default.filters.snp_source."with_variation_annotation"&VISIBLEPANEL=resultspanel > > I get an exception: > > Serious Error: Error during query execution: You have an error in your SQL > syntax; check the manual that corresponds to your MySQL server version for > the right syntax to use near ' > snp_mart_57.hsapiens_snp__variation_feature__main main WHERE (. > 'with_variatio' at line 1 > ERROR: caught BioMart::Exception::Database: Error during query execution: You > have an error in your SQL syntax; check the manual that corresponds to your > MySQL server version for the right syntax to use near ' > snp_mart_57.hsapiens_snp__variation_feature__main main WHERE (. > 'with_variatio' at line 1 > > If you repeatedly get directed to this error page, there may be a problem > with your current session parameters. To clear your session and start with a > clean slate, please click the New button below. > > Stacktrace: > Exception::Class::Base::throw > /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/Dataset/TableSet.pm:241 > BioMart::Dataset::TableSet::_fillAttributeTableWith > /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/Dataset/TableSet.pm:124 > BioMart::Dataset::TableSet::_getResultTable > /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/DatasetI.pm:1170 > BioMart::DatasetI::getResultTable > /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/QueryRunner.pm:472 > BioMart::QueryRunner::_processPath > /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/QueryRunner.pm:374 > BioMart::QueryRunner::_getResultTable > /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/QueryRunner.pm:194 > BioMart::QueryRunner::execute > /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/Web.pm:2433 > (eval) /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/Web.pm:2201 > BioMart::Web::handle_request > /srv/biomart_server/biomart.org/biomart-perl/cgi-bin/martview:99 > (eval) /srv/biomart_server/biomart.org/biomart-perl/cgi-bin/martview:98 > ModPerl::ROOT::ModPerl::Registry::srv_biomart_server_biomart_2eorg_biomart_2dperl_cgi_2dbin_martview::handler > /usr/lib/perl5/ModPerl/RegistryCooker.pm:204 > (eval) /usr/lib/perl5/ModPerl/RegistryCooker.pm:204 > ModPerl::RegistryCooker::run /usr/lib/perl5/ModPerl/RegistryCooker.pm:170 > ModPerl::RegistryCooker::default_handler /usr/lib/perl5/ModPerl/Registry.pm:31 > ModPerl::Registry::handler -e:0 > (eval) -e:0 > > If I uncheck the "with variation annotation" filter, I don't get the > exception. > > Best > Michael > > > Michael Dondrup > Post-doctoral researcher > Uni BCCS > Thormøhlensgate 55, N-5008 Bergen, Norway > >
