[Bioperl-l] bioperl-db question

Tue Nov 21 20:33:10 UTC 2006

Hi Hilmar,

I just rebuilt the Oracle BioSQL database by strictly following the 
INSTALL doc. You are right that BS-create-Biosql-API.sql must be run to 
make bioperl-db work with it(the oid columns). But my installation 
problem was caused by running BS-create-Biosql-API2.sql after it, which 
rendered the database not compatible with bioperl-db. If I ran only 
BS-create-Biosql-API.sql, ll bioperl-db tests could pass. Does this mean 
that the Oracle version is not interoperable between the Bio- projects 
at this point?

Did I miss anything in the INSTALL or README? I only saw a line "-- all 
others (Biojava, etc)" but did not realize I could not run both 
BS-create-Biosql-API.sql and BS-create-Biosql-API2.sql. I this is the 
case, can you please add it to the docs?

Thanks very much for your help.

Gang

Hilmar Lapp wrote:
> 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 :
> ===========================================================
>
>
>
>
>