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

[Rob Syme]

Cool. Just checking that I wasn't struggling with something that was
already known. I'll have a poke around tomorrow.
-r

On 14 Nov 2011 18:43, "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
> > _______________________________________________
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>
>
>