[BioSQL-l] biosql-ora BS-prepopulate-db errors

[Hilmar Lapp]

Sorry, the prepopulate script is old and I believe out of date w.r.t. 
some schema changes. 'Cat_Name' should read 'Ont_Name'. It may work 
after that change.

You will want to carefully review what this script does; it's entirely 
custom and nothing in a plain biosql installation depends on it, nor 
does load_seqdatabase.pl. It populates some early versions of custom 
and small ontologies that make up part of the glue in a Symgene 
database, and may be completely useless for other applications.

Let me know if you really want that content and I'll update the script. 
I also have dagflat versions of some of those ontologies.

	-hilmar

On Jul 22, 2004, at 8:04 AM, Michael Griffith wrote:

> Hi,
>
> I am trying to setup BIOSQL to work with Oracle 9i.  I was able to
> successfully create the database and all of the objects in it.  
> Everything
> seems to be ok, but when I try to execute the prepopulate-db script, I 
> get
> an exception when the script tries to insert into SLGD_Terms.
>
> The sql that causes the exception is:
>
> --
> -- Ontology terms: relationship type ontology
> --
> INSERT INTO SGLD_Terms (Trm_Name, Trm_Identifier, Cat_Name)
> VALUES ('EST','REO:0000345','Relationship Type Ontology');
>
> The exception is:
> ORA-20101: failed to lookup Ont <>
> ORA-06512: at "BIOSQL_APP.TRM" line 102
> ORA-06512: at "BIOSQL_APP.BIR_TERMS" line 6
> ORA-04088: error during execution of trigger "BIOSQL_APP.BIR_TERMS"
>
> Where BIOSQL_APP is my user.  I have looked at the procedures and 
> triggers
> involved, and I see that the exception is being raised from the 
> procedure
> TRM, because of what I think is a broken relationship.
>
> What is confusing to me is that the BS-prepopulate-db.sql script has a
> comment that reads:
>
> -- The following will be created automatically upon inserting their 
> terms.
> --    'Relationship Type Ontology'
> --    'Bioentry Type Ontology'
> --    'Qualifier Type Ontology'
> --
>
> Evidently, this did not happen.  Am I missing something?  Any help 
> would be
> greatly appreciated!
>
> Cheers!
>
> Michael Griffith
>
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-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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