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

[Michael Griffith]

Hilmar, 

Thanks for the reply.

I guess I don't really need it, I was just trying to put some data in the
DB, so I could play with it.  My bigger problem is that once I built the DB
and tried to insert a record using BioJava 1.4, I got a message that the
schema was old and I should have used a new schema.

I posted that message on BioJava mail list, but have received no reply.  Is
this a question you can help me with?

Where can I download the bio-sql-ora scripts that will work with BioJava
1.4?

Thanks in advance!

MG 


On 7/26/04 2:10 PM, "Hilmar Lapp" <hlapp at gnf.org> wrote:

> Sorry, the prepopulate script is old and I believe out of date w.r.t.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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