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

[Raoul Bonnal]

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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