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

[Hilmar Lapp]

I see. You didn't say Biojava and Biosql Oracle in the same sentence 
before did you.

Biojava can't deal with different 'versions' of the same schema even if 
it's only column names, and the Oracle version differs in naming 
conventions. There is an adaptor API in the repository that maps table 
names, but you'll need another one that I've written that maps both 
tables and column names through views. I'll dig that up and post it.

Also, the Biojava folks I believe added a table or a column to one of 
the ontology tables. You'll have to inquire about that on the biojava 
mailing list.

	-hilmar



On Jul 26, 2004, at 12:24 PM, Michael Griffith wrote:

> 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 Sorry, the prepopulate script is old and I believe out of date w.r.t.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
>>>
>>> _______________________________________________
>>> BioSQL-l mailing list
>>> BioSQL-l at open-bio.org
>>> http://open-bio.org/mailman/listinfo/biosql-l
>>>
>
>
-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------