[Bioperl-l] bioperl-db question

Hilmar Lapp hlapp at gmx.net
Tue Nov 21 14:33:11 EST 2006


The Oracle error is

ORA-00904: "BIODATABASE"."OID": invalid identifier

and if you look at the accompanying statement, it's the UK select  
statement:

SELECT <*>biodatabase.oid, biodatabase.name,
biodatabase.authority FROM biodatabase WHERE name = :p1

The column OID must exist in the Biodatabase table (which actually is  
a synonym to the SG_BIODATABASE table), if it is the Oracle schema.

This actually prompts another suggestion, sorry for not asking that  
first: did you actually install the BioSQL-API on top of the schema  
by running the script BS-create-Biosql-API.sql? (It seems that the  
statement it chokes on is also the first statement being prepared, so  
this may well be the reason)

	-hilmar

On Nov 21, 2006, at 3:11 AM, gang wu wrote:

> Can you show me where it indicates I am actually using the MySQL  
> schema.
> I am pretty sure that I used the sql script files from
> sql/biosql-ora(Has anyone actually tried to install MySQL schema on
> Oracle?). I can reinstall the schema if you think that's the way to
> solve the problem.  Thanks very much.
>
> Gang
>
> Hilmar Lapp wrote:
>> It looks like you are using the MySQL schema under Oracle. There are
>> different DDL scripts for each supported RDBMS. The ones for Oracle
>> are in the sql/biosql-ora subdirectory. Note the INSTALL document in
>> that directory.
>>
>> 	-hilmar
>>
>>
>> On Nov 20, 2006, at 1:16 PM, gang wu wrote:
>>
>>
>>> Hi Hilmar,
>>>
>>> Below is the output. Thanks.
>>>
>>> Gang
>>> ==========================================================
>>> [root at elegans bioperl-db-1.5.2-RC3]# export HARNESS_VERBOSE=1
>>> [root at elegans bioperl-db-1.5.2-RC3]# make test_01dbadaptor
>>> TEST_VERBOSE=1
>>> PERL_DL_NONLAZY=1 /usr/bin/perl -Iblib/arch -Iblib/lib -I/usr/lib64/
>>> perl5/5.8.5/x86_64-linux-thread-multi -I/usr/lib/perl5/5.8.5 -e
>>> 'use Test::Harness qw(&runtests $verbose); $verbose=1; runtests
>>> @ARGV;' t/01dbadaptor.t
>>> t/01dbadaptor....1..19
>>> ok 1
>>> ok 2
>>> ok 3
>>> ok 4
>>> ok 5
>>> ok 6
>>> ok 7
>>> ok 8
>>> ok 9
>>> ok 10
>>> ok 11
>>> attempting to load adaptor class for BioNamespace
>>> ok 12
>>>        attempting to load module  
>>> Bio::DB::BioSQL::BioNamespaceAdaptor
>>> instantiating adaptor class Bio::DB::BioSQL::BioNamespaceAdaptor
>>> ok 13
>>> ok 14
>>> attempting to load driver for adaptor class
>>> Bio::DB::BioSQL::BioNamespaceAdaptor
>>> attempting to load driver for adaptor class
>>> Bio::DB::BioSQL::BasePersistenceAdaptor
>>> Using Bio::DB::BioSQL::Oracle::BasePersistenceAdaptorDriver as
>>> driver peer for Bio::DB::BioSQL::BioNamespaceAdaptor
>>> preparing UK select statement: SELECT biodatabase.oid,
>>> biodatabase.name, biodatabase.authority FROM biodatabase WHERE name
>>> = ?
>>> DBD::Oracle::db prepare failed: ORA-00904: "BIODATABASE"."OID":
>>> invalid identifier (DBD ERROR: error possibly near <*> indicator at
>>> char 7 in 'SELECT <*>biodatabase.oid, biodatabase.name,
>>> biodatabase.authority FROM biodatabase WHERE name = :p1') [for
>>> Statement "SELECT biodatabase.oid, biodatabase.name,
>>> biodatabase.authority FROM biodatabase WHERE name = ?"] at blib/lib/
>>> Bio/DB/BioSQL/BaseDriver.pm line 1800.
>>> BioNamespaceAdaptor: binding UK column 1 to "__dummy__" (namespace)
>>> Can't call method "bind_param" on an undefined value at blib/lib/
>>> Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939.
>>> dubious
>>>        Test returned status 255 (wstat 65280, 0xff00)
>>> DIED. FAILED tests 15-19
>>>        Failed 5/19 tests, 73.68% okay
>>> Failed Test     Stat Wstat Total Fail  Failed  List of Failed
>>> -------------------------------------------------------------------- 
>>> --
>>> ---------
>>> t/01dbadaptor.t  255 65280    19   10  52.63%  15-19
>>> Failed 1/1 test scripts, 0.00% okay. 5/19 subtests failed, 73.68%
>>> okay.
>>> make: *** [test_01dbadaptor] Error 2
>>> =========================================================
>>>
>>>
>>> Hilmar Lapp wrote:
>>>
>>>> Hi Gang,
>>>>
>>>> what I wanted to get at was the error message from the driver when
>>>> it fails to generate the prepared statement, but this is not in
>>>> the output.
>>>>
>>>> I believe you need set the HARNESS_VERBOSE environment variable to
>>>> 1 before testing to get what I need:
>>>>
>>>>     $ export HARNESS_VERBOSE=1 # or setenv HARNESS_VERBOSE 1 for
>>>> csh/tcsh
>>>>     $ make test_01dbadaptor TEST_VERBOSE=1
>>>>
>>>> This will lead to _a lot_ of debugging output. Do not run this for
>>>> the entire test suite.
>>>>
>>>> The errors for mysql I believe are related to the fact that have
>>>> loaded the NCBI taxonomy before testing? Run the tests on a fresh
>>>> (completely empty) instance of BioSQL.
>>>>
>>>> Let me know what you get for the Oracle test above.
>>>>
>>>>     -hilmar
>>>>
>>>> On Nov 20, 2006, at 10:57 AM, gang wu wrote:
>>>>
>>>>
>>>>> Hi Hilmar,
>>>>>
>>>>> Thanks for your message. Below are several tests for Oracle and
>>>>> MySQL. MySQL actually also has two tests with failed items which
>>>>> may be related to data in BioSQL database.
>>>>>
>>>>> Could it be my Oracle installation/configuration has some issues?
>>>>>
>>>>> Thanks.
>>>>>
>>>>> Gang
>>>>>
>>>> --===========================================================
>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>> ===========================================================
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>
>>
>
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-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================







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