[ensembl-dev] bug in Search.pm?

[Zhibin Lu]

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
Toronto, Ontario, Canada M5G 0A3
 
Tel: 647-260-7944
Toll-free: 1-866-678-6427
www.oicr.on.ca


 		 	   		  
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