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Hi Fiona,<br><br>I do not think so. It seems that the table alias 'g' is missing in the SQLs and mysql can not find the column of 'stable_id' or 'translation_id'.<br><br>Zhibin<br><br><div>> Date: Tue, 13 Dec 2011 17:50:03 +0000<br>> Subject: Re: [ensembl-dev] bug in Search.pm?<br>> From: fiona@ebi.ac.uk<br>> To: zhbluweb@hotmail.com<br>> CC: dev@ensembl.org; bioinfohelp@oicr.on.ca<br>> <br>> Hi Zhibin,<br>> <br>> This is probably because of the changes in stable_id tables, see blog post:<br>> <br>> http://www.ensembl.info/<br>> <br>> Fiona<br>> <br>> -----------------------------------------------------------------------------------<br>> Fiona Cunningham<br>> Ensembl Coordinator, Ensembl Variation Project Leader.<br>> EMBL-EBI, Genome Campus, Hinxton, UK<br>> www.ensembl.org || www.lrg-sequence.org<br>> fiona@ebi.ac.uk || t: +44 1223 494612<br>> <br>> <br>> <br>> On 13 December 2011 16:54, Zhibin Lu <zhbluweb@hotmail.com> wrote:<br>> > Hi,<br>> ><br>> > I upgraded our Ensembl mirror from release 64 to 65. When I tried to search<br>> > a gene, I got the folllowing error messages in the apache log flie:<br>> ><br>> > DBD::mysql::db selectall_arrayref failed: Unknown column 'g.translation_id'<br>> > in 'where clause' at .../ensembl_65/modules/EnsEMBL/Web/Factory/Search.pm<br>> > line 93.<br>> ><br>> > DBD::mysql::db selectall_arrayref failed: Unknown column 'g.stable_id' in<br>> > 'field list' at .../ensembl_65/modules/EnsEMBL/Web/Factory/Search.pm line<br>> > 93.<br>> ><br>> > I changed line 523 in Search.pm FROM:<br>> > "SELECT concat( display_label ), '$db', 'Transcript', 'peptide' from<br>> > object_xref as ox, xref as x<br>> > TO:<br>> > "SELECT concat( display_label ), '$db', 'Transcript', 'peptide' from<br>> > translation_stable_id as g, object_xref as ox, xref as x<br>> ><br>> > and line 530 in Search.pm FROM:<br>> > "SELECT distinct(g.stable_id), concat( display_label ), '$db', 'Transcript',<br>> > 'peptide' from object_xref as ox, xref as x<br>> > TO:<br>> > "SELECT distinct(g.stable_id), concat( display_label ), '$db', 'Transcript',<br>> > 'peptide' from translation_stable_id as g, object_xref as ox, xref as x<br>> ><br>> > then the browser started working.<br>> ><br>> > Is this a bug?<br>> ><br>> > Thanks,<br>> ><br>> > Zhibin Lu<br>> > Bioinformatics Support: Databases & Applications<br>> ><br>> > Ontario Institute for Cancer Research<br>> > MaRS Centre, South Tower<br>> > 101 College Street, Suite 800<br>> > Toronto, Ontario, Canada M5G 0A3<br>> ><br>> > Tel: 647-260-7944<br>> > Toll-free: 1-866-678-6427<br>> > www.oicr.on.ca<br>> ><br>> ><br>> > _______________________________________________<br>> > Dev mailing list Dev@ensembl.org<br>> > List admin (including subscribe/unsubscribe):<br>> > http://lists.ensembl.org/mailman/listinfo/dev<br>> > Ensembl Blog: http://www.ensembl.info/<br>> ><br></div> </div></body>
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