[BioRuby] BioSQL development

[Rob Syme]

Thanks Toshiaki and Julian,

Mapping features from gff may well become an issue. Until Raoul gets back, I
might try and keep the data under the Chado schema as suggested by Julian.
*If* I can get it clean enough, I'll offer it up for incorporation into
bioruby.

-r


On Sun, Aug 22, 2010 at 4:50 PM, Julian Nordt <ju at ncoffee.de> wrote:

> Hi Rob,
>
> I tried to use the BioSQL part of Bioruby for a webapplication based on
> rails. With the idea of giving users the capability to upload genomes to the
> application. However the mapping between BioSQL <-> GFF3 is(?)/were not
> figured out completly, which was one of the reasons why I changed my
> implementation to CHADO scheme.
>
>
> In regard to your question I did use BioSQL in the following way:
>
>
>  def openBioConnection
>    Bio::SQL.establish_connection(:adapter  => "mysql",
>                                  :host     => "localhost",
>                                  :username => "xxx",
>                                  :password => "xxx",
>                                  :database => "biosql_development")
>  end
>
>
>  def get_sequence(bio_entry_id)
>    openBioConnection()
>    if !bio_entry_id.blank?
>      return Bio::SQL::Biosequence.find_by_bioentry_id(bio_entry_id)
>    end
>  end
>
>
> def setSeqFeatName(id,name)
>    seq_feat = Bio::SQL::Seqfeature.find_by_seqfeature_id(id)
>    Bio::SQL::Seqfeature.update(seq_feat.id, :display_name => name)
>  end
>
> (! This does not mean that it is the correct way or intended way of usage
> as I'm new to ruby/bioruby !)
>
> I had to make some small modifications to
> bio-1.4.0\lib\bio\io\biosql\ar-biosql.rb and biosql.rb, unfortunately I do
> not remember where exactly. Mostlikely some changes in regard to the
> connection adapter and some changes to tablenames or similiar stuff.
>
> As you can see in ar-biosql.rb all the "classes" for the biosql orm are
> already defined, so one does not have to define the classes himself.
>
> Hope this helps,
>
> Julian Nordt
>
>
>
>
>
>
> On Sun, 22 Aug 2010 08:22:18 +0200, Rob Syme <rob.syme at gmail.com> wrote:
>
>  Is there a particular person who has taken charge of the BioSQL part of
>> Bioruby?
>> I just want confirmation that I'm not using it in completely the wrong
>> way.
>>
>> Are the classes designed so that you generate models for an app (a rails
>> app, for example) that inherit from the Bio::SQL::whatever? eg:
>>
>> $ rails g model Biodatabase name:string authority:string description:text
>>
>> and then in app/model/biodatabase.rb you change:
>> class Biodatabase < ActiveRecord::Base
>> end
>>
>> into:
>> class Biodatabase < Bio::SQL::Biodatabase # which inherits
>> ActiveRecord::Base
>> end
>>
>> If I get a handle on this, I'd be happy to write it up for
>> http://bioruby.open-bio.org/wiki/Tutorial#BioSQL
>>
>> Thanks for all the work by the dev team. Much appreciated - I use bioruby
>> almost every day.
>> -r
>>
>> Rob Syme
>> _______________________________________________
>> BioRuby Project - http://www.bioruby.org/
>> BioRuby mailing list
>> BioRuby at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioruby
>>
>>
>
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