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
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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
