[ensembl-dev] adding a new specie

[oreetseng at sanbi.ac.za]

Anne and Will, thanks a lot for your help!
The problem has been fixed,

Regards,
Oreetseng.


> 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
>>
>>
>>
>>
>> _______________________________________________
>> Dev mailing list    Dev at ensembl.org
>> List admin (including subscribe/unsubscribe):
>> http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog: http://www.ensembl.info/
>>
>
>
> --
>  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.
>