[ensembl-dev] bug in Search.pm?

[Fiona Cunningham]

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
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> 101 College Street, Suite 800
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>
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>
>
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