<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Have sent this to the list once, but it didn't get a reply and it isn't showing up in the archives, so I'll try again:</div><div><br></div>I'm trying to do a biomaRt query and I seem to be throwing errors on protists_mart_12 that weren't there in protists_mart_10. <div>In particular 'entrezgene' has disappeared from berghei, and is present in falciparum:</div><div><br></div><div></div><blockquote type="cite"><div>> subset(listAttributes(useMart("protists_mart_12",dataset="pfalciparum_eg_gene")),name=="entrezgene")</div><div> name description</div><div>28 entrezgene EntrezGene ID</div><div>> subset(listAttributes(useMart("protists_mart_12",dataset="pberghei_eg_gene")),name=="entrezgene")</div><div>[1] name description</div><div><0 rows> (or 0-length row.names)</div></blockquote><div> </div><div>Attempting to run a query (falciparum, entrezgene) on martview suggests it's been removed from the mart schema, but not from the front-end (see error message below). I don't think I see anything in the release notes about removing entrezgenes, so is this likely to be fixed before next release?</div><div><br></div><div>thanks</div><div><br></div><div>-s</div><div><br></div><div><br></div><div><br></div><div><div id="resultspanel" style="width: 811px; height: 443px; overflow-x: hidden; overflow-y: hidden; position: relative; display: block; "><blockquote type="cite"><table width="100%" height="100%" border="0" cellpadding="0" cellspacing="0" style="table-layout: fixed; "><tbody><tr><td width="100%" height="100%" valign="top" align="left"><div id="mart_export_data" style="color: black; background-color: white; width: 811px; height: 319px; overflow-x: auto; overflow-y: auto; "><table width="100%" height="100%" border="0" cellpadding="" cellspacing="0" style="table-layout: auto; position: static; z-index: auto; "><tbody><tr><td id="resultsTableId" width="100%" height="100%" valign="top" align="left">Serious Error: Error during query execution: Unknown column 'protists_mart_12.pfalciparum_eg_gene__ox_entrezgene__dm.translation_id_1068_key' in 'where clause'<p>ERROR: caught BioMart::Exception::Database: Error during query execution: Unknown column 'protists_mart_12.pfalciparum_eg_gene__ox_entrezgene__dm.translation_id_1068_key' in 'where clause'<br></p><p>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 <b>New</b> button below.</p><p>Stacktrace:<br>Exception::Class::Base::throw /net/isilonP/public/rw/ensembl/ensembl-genomes/release-12/biomarts/protists/biomart-perl/lib/BioMart/Dataset/TableSet.pm:241<br>BioMart::Dataset::TableSet::_fillAttributeTableWith /net/isilonP/public/rw/ensembl/ensembl-genomes/release-12/biomarts/protists/biomart-perl/lib/BioMart/Dataset/TableSet.pm:124<br>BioMart::Dataset::TableSet::_getResultTable /net/isilonP/public/rw/ensembl/ensembl-genomes/release-12/biomarts/protists/biomart-perl/lib/BioMart/DatasetI.pm:1170<br>BioMart::DatasetI::getResultTable /net/isilonP/public/rw/ensembl/ensembl-genomes/release-12/biomarts/protists/biomart-perl/lib/BioMart/QueryRunner.pm:472<br>BioMart::QueryRunner::_processPath /net/isilonP/public/rw/ensembl/ensembl-genomes/release-12/biomarts/protists/biomart-perl/lib/BioMart/QueryRunner.pm:374<br>BioMart::QueryRunner::_getResultTable /net/isilonP/public/rw/ensembl/ensembl-genomes/release-12/biomarts/protists/biomart-perl/lib/BioMart/QueryRunner.pm:194<br>BioMart::QueryRunner::execute /net/isilonP/public/rw/ensembl/ensembl-genomes/release-12/biomarts/protists/biomart-perl/lib/BioMart/Web.pm:2429<br>(eval) /net/isilonP/public/rw/ensembl/ensembl-genomes/release-12/biomarts/protists/biomart-perl/lib/BioMart/Web.pm:2197<br>BioMart::Web::handle_request /net/isilonP/public/rw/ensembl/ensembl-genomes/release-12/biomarts/protists/biomart-perl/cgi-bin/martview:107<br>(eval) /net/isilonP/public/rw/ensembl/ensembl-genomes/release-12/biomarts/protists/biomart-perl/cgi-bin/martview:106<br>ModPerl::ROOT::ModPerl::Registry::net_isilonP_public_rw_ensembl_ensembl_2dgenomes_release_2d12_biomarts_protists_biomart_2dperl_cgi_2dbin_martview::handler /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:204<br>(eval) /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:204<br>ModPerl::RegistryCooker::run /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:170<br>ModPerl::RegistryCooker::default_handler /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/Registry.pm:31<br>ModPerl::Registry::handler -e:0<br>(eval) -e:0</p></td></tr></tbody></table></div></td></tr></tbody></table></blockquote></div></div><div><br></div><br><br><div apple-content-edited="true">
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>--</div><div>Seth Redmond</div><div> Unité de Genetique et Genomique des Insectes Vecteurs<br> Institut Pasteur<br> 28,rue du Dr Roux<br> 75724 PARIS<br></div><div><a href="mailto:seth.redmond@pasteur.fr">seth.redmond@pasteur.fr</a></div></div></span></span>
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