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.
