Hi Rhoda and Christina, thank you for this information. I can confirm that the query works in ensembl mart.
Best Michael Dondrup Post-doctoral researcher Uni BCCS Thormøhlensgate 55, N-5008 Bergen, Norway Am Mar 9, 2010 um 5:41 PM schrieb Rhoda Kinsella: > Hi Michael and Christina > We have had to patch the ensembl and snp mart meta tables to fix a few bugs > that were reported post release. Christina, if you re-configure the > www.biomart.org site, these new changes will be picked up. Apologies for any > inconvenience caused. Michael, you should temporarily point to > www.ensembl.org until the www.biomart.org site has been re-configured to use > the new meta tables. > Regards > Rhoda > > > On 9 Mar 2010, at 15:54, Christina Yung wrote: > >> Hi Michael: >> >> Thanks for letting us know of the problem. We're looking into it and will >> provide updates soon. In the mean time, please try accessing Ensembl >> (http://www.ensembl.org/biomart/martview/) which is working for your >> particular query. >> >> Regards, >> Christina Yung >> Scientist/Computational Biologist >> >> Ontario Institute for Cancer Research >> MaRS Centre, South Tower >> 101 College Street, Suite 800 >> Toronto, Ontario, Canada M5G 0A3 >> Tel: 416-673-8578 >> >> >>> -----Original Message----- >>> From: [email protected] >>> [mailto:[email protected]] On Behalf Of Michael Dondrup >>> Sent: Tuesday, March 09, 2010 9:54 AM >>> To: [email protected] >>> Subject: [mart-dev] Error in Martview query >>> >>> 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=defa >> ult&ATTRIBUTES=hsapiens_snp.default.snp.refsnp_id|hsapiens_snp.default.snp.chr_name|hsapiens_snp.> >> default.snp.chrom_start&FILTERS=hsapiens_snp.default.filters.s >>> np_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/Datas >>> et/TableSet.pm:241 >>> BioMart::Dataset::TableSet::_fillAttributeTableWith >>> /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/Datas >>> et/TableSet.pm:124 >>> BioMart::Dataset::TableSet::_getResultTable >>> /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/Datas >>> etI.pm:1170 >>> BioMart::DatasetI::getResultTable >>> /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/Query >>> Runner.pm:472 >>> BioMart::QueryRunner::_processPath >>> /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/Query >>> Runner.pm:374 >>> BioMart::QueryRunner::_getResultTable >>> /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/Query >>> Runner.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_2 >>> eorg_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 >>> >>> >>> >>> > > Rhoda Kinsella Ph.D. > Ensembl Bioinformatician, > European Bioinformatics Institute (EMBL-EBI), > Wellcome Trust Genome Campus, > Hinxton > Cambridge CB10 1SD, > UK. >
