[ensembl-dev] bug in Search.pm?

[Andy Yates]

Hi,

It does seem that there is an error in the SQL. I've committed a fix to the branch & to HEAD.

Thank you for finding the error

Andy

On 13 Dec 2011, at 18:00, Zhibin Lu wrote:

> Hi Fiona,
> 
> 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'.
> 
> Zhibin
> 
> > Date: Tue, 13 Dec 2011 17:50:03 +0000
> > Subject: Re: [ensembl-dev] bug in Search.pm?
> > From: fiona at ebi.ac.uk
> > To: zhbluweb at hotmail.com
> > CC: dev at ensembl.org; bioinfohelp at oicr.on.ca
> > 
> > Hi Zhibin,
> > 
> > This is probably because of the changes in stable_id tables, see blog post:
> > 
> > http://www.ensembl.info/
> > 
> > Fiona
> > 
> > -----------------------------------------------------------------------------------
> > Fiona Cunningham
> > Ensembl Coordinator, Ensembl Variation Project Leader.
> > EMBL-EBI, Genome Campus, Hinxton, UK
> > www.ensembl.org || www.lrg-sequence.org
> > fiona at ebi.ac.uk   || t: +44 1223 494612
> > 
> > 
> > 
> > On 13 December 2011 16:54, Zhibin Lu <zhbluweb at hotmail.com> wrote:
> > > Hi,
> > >
> > > I upgraded our Ensembl mirror from release 64 to 65. When I tried to search
> > > a gene, I got the folllowing error messages in the apache log flie:
> > >
> > > DBD::mysql::db selectall_arrayref failed: Unknown column 'g.translation_id'
> > > in 'where clause' at .../ensembl_65/modules/EnsEMBL/Web/Factory/Search.pm
> > > line 93.
> > >
> > > DBD::mysql::db selectall_arrayref failed: Unknown column 'g.stable_id' in
> > > 'field list' at .../ensembl_65/modules/EnsEMBL/Web/Factory/Search.pm line
> > > 93.
> > >
> > > I changed line 523 in Search.pm FROM:
> > > "SELECT concat( display_label ), '$db', 'Transcript', 'peptide' from
> > > object_xref as ox, xref as x
> > > TO:
> > > "SELECT concat( display_label ), '$db', 'Transcript', 'peptide' from
> > > translation_stable_id as g, object_xref as ox, xref as x
> > >
> > >  and line 530 in Search.pm FROM:
> > > "SELECT distinct(g.stable_id), concat( display_label ), '$db', 'Transcript',
> > > 'peptide' from object_xref as ox, xref as x
> > > TO:
> > > "SELECT distinct(g.stable_id), concat( display_label ), '$db', 'Transcript',
> > > 'peptide' from translation_stable_id as g, object_xref as ox, xref as x
> > >
> > > then the browser started working.
> > >
> > > Is this a bug?
> > >
> > > Thanks,
> > >
> > > Zhibin Lu
> > > Bioinformatics Support: Databases & Applications
> > >
> > > Ontario Institute for Cancer Research
> > > MaRS Centre, South Tower
> > > 101 College Street, Suite 800
> > > Toronto, Ontario, Canada M5G 0A3
> > >
> > > Tel: 647-260-7944
> > > Toll-free: 1-866-678-6427
> > > www.oicr.on.ca
> > >
> > >
> > > _______________________________________________
> > > Dev mailing list    Dev at ensembl.org
> > > List admin (including subscribe/unsubscribe):
> > > http://lists.ensembl.org/mailman/listinfo/dev
> > > Ensembl Blog: http://www.ensembl.info/
> > >
> _______________________________________________
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---
Andrew Yates                   Ensembl Core Software Project Leader
EMBL-EBI                       Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensembl.org/