Re: [SBEAMS-devel] problem with GO install

[Luis M <rea...@ya...>]

Hello,
I have not installed this linking in mySQL yet; only on MS-SQL.

From taking a quick look at those sql files, it seems that some
just need the semicolon delimiter appended to each statement, 
and the "dbo." prefix removed.  Perhaps you could try this and
see how far you get?  We can include your findings in a future
revision of the install notes or scripts.

Thanks,
--Luis


--- Dave Campbell <dca...@sy...> wrote:

> Jeff;
> 
>   You are right, there is some SQLServer specific syntax in most if not 
> all of the listed files.  There was some talk about moving the table 
> definitions in to the BioLink table/column properties files, which would
> 
> allow the db-appropriate SQL syntax to be produced by 
> generate_schema.pl.  At the very least, we should rename the files using
> 
> our current convention, where the .sql suffix denotes a 'neutral-syntax'
> 
> file, .mssql denotes SQL server syntax (e.g. the GO files) and .mysql 
> denotes mysql syntax.
> 
> I have never installed the GO annotation tables from these files, either
> 
> on mssql or mysql.  Luis, have you had occasion to do so?  In the short 
> term you'll probably have to edit the file manually.
> 
> -Dave
> 
> >Hi, Eric and Dave -
> >
> >I have run into a roadblock trying to install the GeneOntology database
> under MySQL 5.0 on my Linux box.  After a couple of partition-sizing
> mishaps, I got through Section 1 of the GeneOntology.installnotes
> (Download and import the Gene Ontology data) in good shape.  In Section
> 2 (Run gene_annotation scripts in BioLink), however, it seems the
> scripts are still limited to dealing with a SQL Server database.  For
> example, processing the first SQL script listed gives this error:
> >
> >[jhowbert@localhost sbeams]$ $SBEAMS/lib/scripts/Core/runsql.pl --user
> sbeamsadmin --sfile
> $SBEAMS/lib/sql/BioLink/BioLink_GOAnnotation_DROPTABLES.sql --database
> $BIOLINK_DATABASE --delimiter semicolon
> >Enter password, followed by [Enter] (cntl-C to quit):   
> >DBD::mysql::db do failed: You have an error in your SQL syntax; check
> the manual that corresponds to your MySQL server version for the right
> syntax to use near 'DROP TABLE gene_annotation
> >DROP TABLE gene_annotation_type
> >DRO at /var/www/html/dev1/sbeams/lib/scripts/Core/runsql.pl line 130,
> <FIL> line 14.
> >
> >The outcome is the same whether or not I include the --delimiter
> switch.
> >
> >The SQL scripts BioLink_GOAnnotation_DROPTABLES.sql and
> BioLink_GOAnnotation_CREATETABLES.sql are clearly written in the SQL
> Server dialect.  Have you performed a full GeneOntology install under
> MySQL?  If so, did you have to do things that are not documented in
> GeneOntology.installnotes?  Thanks.
> >
> >Jeff Howbert
> >
> >
> >
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