[ensembl-dev] EnsemblGenomes search error

[Nick Langridge]

Hi Gang Chen,

It looks like the default Esnembl search plugin is not compatible with 
Ensembl Bacteria when searching a single species. If you are mirroring 
the Ensembl Bacteria data you may want to try connecting to the EBI 
search webservice using the EBEye search plugin.

The plugin is in CVS here 
http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/eg-plugins/ebeye-search/?root=ensembl

To install...

1. check out the plugin code into you eg-plugins dir E.g.

$ cd <your-server-root>
$ cvs co -r branch-ensemblgenomes-16-69 eg-plugins/ebeye-search

2. add (or un-comment) the following line in your plugins file 
(<your-server-root>/conf/Plugins.pm)

   'EG::EBEyeSearch'         => 
$SiteDefs::ENSEMBL_SERVERROOT.'/eg-plugins/ebeye-search',

The EG::EBEyeSearch plugin should be above the EG::Bacteria plugin in 
the file.

3. configure the search endpoint by adding the following lines to 
<your-server-root>/my-plugins/conf/ini-files/DEFAULTS.ini

[general]
EBEYE_ENDPOINT = http://www.ebi.ac.uk/ebisearch/service.ebi

4. Restart your server.

You should now have full search functionality.

Please let me know if this solves your problem of if there is anything 
else you need.

Thanks
Nick




On 04/01/2013 02:32, ?? wrote:
> Hi All
>
> Our EnsemblGenomes mirror suffers a search error. For instance, search 
> dnaA in species Escherichia coli K12, the mirror returns 12 entries.
>
> Gene: EBESCG00000003429 [Region in detail]
> Gene: EBESCG00000007452 [Region in detail]
> Gene: EBESCG00000013460 [Region in detail]
> Gene: EBESCG00000018762 [Region in detail]
> Gene: EBESCG00000023601 [Region in detail]
> Gene: EBESCG00000031974 [Region in detail]
> Gene: EBESCG00000037518 [Region in detail]
> Gene: EBESCG00000048558 [Region in detail]
> Gene: EBESCG00000052321 [Region in detail]
> Gene: EBESCG00000057553 [Region in detail]
> Gene: EBESCG00000003435 [Region in detail]
> Gene: EBESCG00000002586 [Region in detail]
>
> However, some linkages of these entries are unavailable, report a 
> internal page error, including
> EBESCG00000007452
> EBESCG00000013460
> EBESCG00000018762
> EBESCG00000023601 and so on.
>
> I checked above IDs from tables ensembl_compara_bacteria_16_69.member 
> and ensembl_compara_bacteria_16_69.genome_db, they are not belong to 
> species Escherichia coli K12, 
> but e_coli_atcc_8739, e_coli_atcc_27325, e_coli_o139_h28, e_coli_edl933 respectively.
>
> If change the URLs which return the internal error with above names, 
> they work correctly. For example, change
> http://172.16.10.16:8899/e_coli_k12/Gene/Summary?g=EBESCG00000007452;db=core
> to
> http://172.16.10.16:8899/e_coli_atcc_8739/Gene/Summary?db=core;g=EBESCG00000007452
>
> Therefore, the search error is caused by wrong species name which is 
> applied as a part of URL. Could you fix the error?
>
> Best regards
>
> -- 
> Gang Chen
> TILSI
> Taicang Institute For Life Science Information
> Address: A2/162, Renmin South Road, Taicang, 215400, Jiangsu Province, 
> P.R.China
> Phone:(+86)512-82782588
>
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20130107/aa75a5f7/attachment.html>