[ensembl-dev] bug in Search.pm?

[Zhibin Lu]

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
> >
> >
> > _______________________________________________
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> > Ensembl Blog: http://www.ensembl.info/
> >
 		 	   		  
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