[ensembl-dev] adding a new specie

[Will Chow]

Hi,

Annes suggestion of removing the packed files 
(conf/packed/[species].db*) and config.packed file is a good start.  
Another check is to see in the meta table, do you have the 
species_alias_name and if so, check to see that the species_id for that 
entry is not NULL. 

eg)
| meta_id | species_id | meta_key                   | 
meta_value                                                                    
|
|      49 |          1 | species.ensembl_alias_name | SPECIES A 
                                                           |

Those are some of the quick things off the top of my head.

Will

Anne Parker wrote:
> On 8 Nov 2011, at 15:02, oreetseng at sanbi.ac.za wrote:
>
>   
>> Hi Anne,
>>
>> The first part is fixed (search on the front page), i have also added the
>> species.ensembl_alias_name value, I still get the same complaint, with the
>> specie name not appearing:
>>
>> "multi is not a valid species name for this instance
>> Use of uninitialized value $common in hash element at
>> fungi/eg-plugins/common/modules/EnsEMBL/Web/Document/HTML/SpeciesPage.pm
>> line 39"
>>     
>
> As this is in the EnsemblGenomes plugin, I don't have immediate access to a copy, and don't know what changes the EG team have made. Perhaps you could contact them if the problem persists?
>
> One final thought - if you've changed the database, you need to delete the .db.packed file as well as config.packed when you restart your server.
>
> Cheers
>
> Anne
>
>   
>> I am proof checking the modifications made to the files and will keep you
>> posted,
>>
>> Thanx a lot!!
>> Oreetseng
>>
>>
>>
>>
>>     
>>> Hi Oreetseng
>>>
>>> It looks as though your species configuration is incomplete somewhere.
>>>
>>> On 7 Nov 2011, at 17:52, oreetseng at sanbi.ac.za wrote:
>>>
>>>       
>>>> Hi all ,
>>>>
>>>> I want to add a new specie to the ensembl local core database, i have
>>>> configured all the important files as per ensembl documentation guide.
>>>>
>>>> On the front page the local mirror, my_specie picture shows, but unlike
>>>> other fungal species there is no name next to the picture and when i
>>>> click
>>>> on the picture the error appears that reads: "Search
>>>> .Runtime Error in component "EnsEMBL::Web::Component::Info::Summary
>>>> [content]"
>>>> Function EnsEMBL::Web::Component::Info::Summary fails to execute due to
>>>> the following error:
>>>> Can't use an undefined value as a HASH reference at
>>>> fungi/modules/EnsEMBL/Web/Document/HTML/HomeSearch.pm line 80 "
>>>>         
>>> Please compare the .ini file for your new species to the Ensembl ones - at
>>> the end of the file there should be a block defining sample entry points.
>>> Here's the equivalent for yeast:
>>>
>>> [SAMPLE_DATA]
>>> LOCATION_PARAM    = IV:366098-466099
>>> LOCATION_TEXT     = IV:366098-466099
>>>
>>> GENE_PARAM        = YGR147C
>>> GENE_TEXT         = NAT2
>>>
>>> TRANSCRIPT_PARAM  = YGR147C
>>> TRANSCRIPT_TEXT   = NAT2
>>>
>>> VARIATION_PARAM   = s02-316976
>>> VARIATION_TEXT    = s02-316976
>>>
>>> SEARCH_TEXT       = alcohol dehydrogenase
>>>
>>> I will fix the code so that absence of this data does not cause an error,
>>> but I recommend populating these values anyway.
>>>
>>>       
>>>> on the taillog the error reads as follows:
>>>> multi is not a valid species name for this instance
>>>> Can't use an undefined value as a HASH reference at
>>>> /fungi/modules/EnsEMBL/Web/Document/HTML/HomeSearch.pm line 80.
>>>> Use of uninitialized value $common in hash element at
>>>> fungi/eg-plugins/common/modules/EnsEMBL/Web/Document/HTML/SpeciesPage.pm
>>>> line 39.
>>>>         
>>> The error here seems to be that no common name is being picked up by the
>>> web code (hence the absence of a link next to the picture). Please check
>>> that your database contains a meta entry called species.ensembl_alias_name
>>> - the value can be the scientific name or the common name, whichever you
>>> prefer to display.
>>>
>>> Let me know how you get on.
>>>
>>> Cheers
>>>
>>> Anne
>>>
>>>
>>> Anne Parker
>>> Ensembl Web Production Manager
>>> http://www.ensembl.org
>>>
>>>
>>>
>>>
>>>
>>> --
>>> The Wellcome Trust Sanger Institute is operated by Genome Research
>>> Limited, a charity registered in England with number 1021457 and a
>>> company registered in England with number 2742969, whose registered
>>> office is 215 Euston Road, London, NW1 2BE.
>>>
>>>       
>>     
>
> Anne Parker
> Ensembl Web Production Manager
> http://www.ensembl.org
>
>
>
>
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