To clarify, I was using the Martview web-interface for building and executing this query, and the perl/MySQL output was displayed on the result web-page.
Am Mar 9, 2010 um 5:31 PM schrieb jorge zamora: > 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 >> >> > >
