Hi Younghoon, > the problem seems to be with the misconfigured Reactome mart. The > 'interaction_num_key' is missing. > I have cc'ed Robin Haw from Reactome who should be able to answer this > question. > > In the future please direct your queries against www.biomart.org rather > than reactome directly. We make sure that all backwards compatibility issues > are corrected there. The www.biomart.org server provides a unified access > to all BioMart databases including Reactome > > > a > > > > > > On Fri, Oct 21, 2011 at 11:57 PM, Younghoon Kim <[email protected]> wrote: > >> >> The error message was like below. Please consider it. >> Younghoon Kim >> >> >> -------------------------------------------------------------------------------------------------------------- >> >> Serious Error: >> >> Query error occurred at web service based data source! >> >> Remote data source: http://reactome.oicr.on.ca:5555/biomart/martservice? >> >> Query XML: >> <?xml version="1.0" encoding="UTF-8"?> >> <!DOCTYPE Query> >> <Query virtualSchemaName = "default" limitStart = "" limitSize = "200" >> count = "" softwareVersion = "0.6" requestId= "biomart-client"> >> <Dataset name = "interaction" interface = "default" > >> <Attribute name = "interaction_num_key" /> >> <Attribute name = "protein1_concat" /> >> <Attribute name = "protein2_concat" /> >> </Dataset> >> </Query> >> >> Please ensure the above query XML is well-formed and does not contain >> illegal characters. >> >> Error message from remote server as below: >> Query ERROR: caught BioMart::Exception::Usage: Attribute interaction_num_key >> NOT FOUND >> >> ERROR: caught BioMart::Exception::Query: >> >> Query error occurred at web service based data source! >> >> Remote data source: http://reactome.oicr.on.ca:5555/biomart/martservice? >> >> >> Query XML: >> <?xml version="1.0" encoding="UTF-8"?> >> <!DOCTYPE Query> >> <Query virtualSchemaName = "default" limitStart = "" limitSize = "200" >> count = "" softwareVersion = "0.6" requestId= "biomart-client"> >> >> >> <Dataset name = "interaction" interface = "default" > >> <Attribute name = "interaction_num_key" /> >> <Attribute name = "protein1_concat" /> >> <Attribute name = "protein2_concat" /> >> >> >> </Dataset> >> </Query> >> >> Please ensure the above query XML is well-formed and does not contain >> illegal characters. >> >> Error message from remote server as below: >> Query ERROR: caught BioMart::Exception::Usage: Attribute interaction_num_key >> NOT FOUND >> >> 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/Configuration/URLLocation.pm:110 >> BioMart::Configuration::URLLocation::getResultSet /srv/biomart_server/ >> biomart.org/biomart-perl/lib/BioMart/Dataset/TableSet.pm:206 >> 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:96 >> (eval) /srv/biomart_server/biomart.org/biomart-perl/cgi-bin/martview:95 >> 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 >> >> On Fri, Oct 21, 2011 at 11:04 PM, Arek Kasprzyk >> <[email protected]>wrote: >> >>> Dear Younghoon, >>> Please send us more details about the error. I am cc'ing >>> [email protected] so someone from Reactome will be able to help you >>> >>> a >>> >>> >>> On Fri, Oct 21, 2011 at 5:11 AM, Younghoon Kim <[email protected]> wrote: >>> >>>> >>>> >>>> Dear Arek Kasprzyk, >>>> >>>> >>>> Thanks for managing the biomart system, which has been very useful to >>>> our studies. >>>> In using it, I faced some problem. When I use the reactome's >>>> 'interaction', then some error occurred. Please consider it. >>>> >>>> >>>> Sincerely, >>>> >>>> >>>> >>>> Younghoon Kim >>>> Dept. of Bio and Brain Engineering >>>> KAIST, South Korea >>>> >>>> >>>> >>>> >>> >> >
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