Re: [GUSDEV] plugins

[Isabelle P. <isa...@sb...>]

Thanks for your help, Elisabetta, much appreciated. 

I've managed to load the GO terms. Just in case another GUS on Postgres
user wants to do the same, here is what I did:

- edit InsertGeneOntology.pm: go_tc table definition, replace NUMBER
type with INTEGER
- create the actual go_tc table in the PUBLIC schema (the plugin issues
a DROP command, which will fail and cause the programme to go into an
endless loop)

ALTER TABLE GOSynonym ALTER COLUMN text TYPE varchar(1000);
ALTER SEQUENCE SRes.ExternalDatabase_sq restart with 3027;

$ wget http://www.geneontology.org/ontology/gene_ontology.obo

$ ga GUS::Supported::Plugin::InsertExternalDatabase --name 'GO ontology'
--commit   

$ ga GUS::Supported::Plugin::InsertExternalDatabaseRls --databaseName
'GO ontology' --releaseDate '2008-12-12' --databaseVersion '4.514'
--downloadUrl 'http://www.geneontology.org/ontology/gene_ontology.obo'
--commit 

$ ga GUS::Supported::Plugin::InsertGeneOntology
--oboFile=gene_ontology.obo --extDbRlsName="GO ontology"
--extDbRlsVer="4.514" --commit


Isabelle

--
Isabelle Phan, DPhil
Seattle Biomedical Research Institute
+1(206)256 7113
 

> -----Original Message-----
> From: Elisabetta Manduchi [mailto:man...@pc...] 
> Sent: Monday, December 15, 2008 5:17 PM
> To: Isabelle Phan
> Cc: gus...@li...
> Subject: Re: plugins
> 
> 
> Hi Isabelle,
> you don't need to check in svn to test private plugins. You 
> modify your 
> plugin in your $PROJECT_HOME and build $GUS_HOME.
> To test the plugin you can run it in non-commit mode. If you 
> want to test 
> and commit, by appropriately changing the Revision number of 
> the plugin 
> in $GUS_HOME you should be able to hack it to think that it has been 
> checked in.
> Elisabetta
> 
> On Mon, 15 Dec 2008, Isabelle Phan wrote:
> 
> > How do I test private (ie my own) plugins?
> >
> > I cannot load GO terms because the table definition for the 
> temporary
> > load table is broken for Postgres.
> >
> > I updated the InsertGeneOntology plugin, but I don't want 
> to check it
> > into subversion, because it will break for the default Oracle
> > implementation.
> >
> > At the moment I am competely stuck, and appreciate any help,
> >
> > Thanks
> >
> > Isabelle
> >
> >> I rejoiced too soon....
> >>
> >> There is a problem with the GO plugin, after the GO terms have been
> >> loaded, I am getting:
> >>
> >> Transitive closure (length 4000418): added 0 edges
> >> DBD::Pg::st execute failed: ERROR:  prepared statement 
> "dbdpg_2" does
> >> not exist
>