[BioRuby] BioSQL - postgres refusing SQL generated by Bio::SQL::establish_connection

[Naohisa GOTO]

Hi Raoul,

Which version of ActiveRecord is suitable with the current
BioRuby's biosql implementation?

With RubyGems and (optionally) with Bundler, we can specify
specific version number to be used.

Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org

On Mon, 14 Nov 2011 11:43:51 +0100
Raoul Bonnal <bonnal at ingm.org> wrote:

> Hi Rob,
> may be a problem of my biosql implementation, I suppose.
> I didn't update the library and I didn't check compatibility with new active
> record stuff and composite primary keys.
> Now, I can not take care of this, if there is someone wants to take care of
> I'll be happy to support him/her.
> 
> 
> On 14/11/11 07.07, "Rob Syme" <rob.syme at gmail.com> wrote:
> 
> > Hi all,
> > Full details are up at: http://gist.github.com/1363302
> > 
> > This might just be the result of a schema change in BioSQL, but my SQL
> > knowledge doesn't extend quite far enough. Has anyone come across this
> > before?
> > 
> > When connecting to an empty postgres BioSQL db, I get an
> > ActiveRecord::StatementInvalid error:
> > 
> > PGError: ERROR:  cannot perform INSERT RETURNING on relation "ontology"
> > HINT:  You need an unconditional ON INSERT DO INSTEAD rule with a
> > RETURNING clause.
> > : INSERT INTO "ontology" ("definition", "name") VALUES ($1, $2)
> > RETURNING "ontology_id"
> > ActiveRecord::StatementInvalid: PGError: ERROR:  cannot perform INSERT
> > RETURNING on relation "ontology"
> > HINT:  You need an unconditional ON INSERT DO INSTEAD rule with a
> > RETURNING clause.
> > : INSERT INTO "ontology" ("definition", "name") VALUES ($1, $2)
> > RETURNING "ontology_id"
> > from 
> > /home/rob/.rvm/gems/ruby-1.9.2-p290/gems/activerecord-3.1.1/lib/active_record/
> > connection_adapters/postgresql_adapter.rb:1009:in
> > `prepare'
> > <snip>
> > from 
> > /home/rob/.rvm/gems/ruby-1.9.2-p290/gems/bio-1.4.2.5000/lib/bio/io/biosql/bios
> > ql.rb:31:in
> > `establish_connection'
> > 
> > 
> > The offending SQL was:
> > 
> > SELECT "ontology".* FROM "ontology" WHERE (name = 'Annotation Tags')
> > LIMIT 1 # This works fine
> > INSERT INTO "ontology" ("definition", "name") VALUES ($1, $2)
> > RETURNING "ontology_id"  [["definition", nil], ["name", "Annotation
> > Tags"]] # This fails
> > 
> > Relevant gems installed:
> >   activerecord (3.1.1)
> >   composite_primary_keys (4.1.1)
> >   pg (0.11.0)
> >   bio (1.4.2.5000)
> > 
> > Using:
> >   psql (PostgreSQL) 9.1.1
> >   BioSQL schema version 1.0.1 and
> >   ruby 1.9.2p290 (2011-07-09 revision 32553) [x86_64-linux]
> > 
> > -r
> > _______________________________________________
> > 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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