[BioSQL-l] Re: [Bioperl-l] Biosql schema for use w/ bioperl-1.2.1

Hilmar Lapp hlapp at gnf.org
Tue Apr 22 15:21:04 EDT 2003 

On Tuesday, April 22, 2003, at 01:30  PM, Steve Mathias wrote:

> Hilmar,
>
> I'm now using the latest CVS versions of both biosql-schema and
> bioperl-db.  Several bioperl-db tests fail with messages about table
> biosql.taxon_name not existing, which indeed it does not (the version  
> of
> biosqldb-mysql.sql that I just checked out has: -- $Id:
> biosqldb-mysql.sql,v 1.21 2003/02/17 09:50:35 lapp Exp $)
>

This is not the latest revision. It actually is the  
before-singapore-change version. You need to pull out the HEAD of cvs,  
not any branch. The current version of the mysql DDL file is 1.34.

Likewise with bioperl-db. Pull out the HEAD, not any tagged branch.

	-hilmar


> Here is the output of the species test:
>
> smathias at poblano 1224 > make test_species TEST_VERBOSE=1
> PERL_DL_NONLAZY=1 /usr/local/bin/perl -Iblib/arch -Iblib/lib  
> -I/usr/local/lib/perl5/5.6.1/i686-linux -I/usr/local/lib/perl5/5.6.1  
> -e 'use Test::Harness qw(&runtests $verbose); $verbose=1; runtests  
> @ARGV;' t/species.t
> t/species....1..65
> ok 1
> ok 2
> ok 3
> ok 4
> ok 5
> DBD::mysql::st execute failed: Table 'biosql.taxon_name' doesn't exist  
> at blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 892.
>
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: error while executing statement in  
> Bio::DB::BioSQL::SpeciesAdaptor::find_by_unique_key: Table  
> 'biosql.taxon_name' doesn't exist
> STACK: Error::throw
> STACK: Bio::Root::Root::throw  
> /usr/local/lib/perl5/site_perl/5.6.1/Bio/Root/Root.pm:342
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key  
> blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:898
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key  
> blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:809
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create  
> blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:180
> STACK: Bio::DB::Persistent::PersistentObject::create  
> blib/lib/Bio/DB/Persistent/PersistentObject.pm:242
> STACK: t/species.t:35
> -----------------------------------------------------------
> dubious
>         Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 6-65
>         Failed 60/65 tests, 7.69% okay
> Failed Test Stat Wstat Total Fail  Failed  List of Failed
> ----------------------------------------------------------------------- 
> --------
> t/species.t  255 65280    65   60  92.31%  6-65
> Failed 1/1 test scripts, 0.00% okay. 60/65 subtests failed, 7.69% okay.
> make: *** [test_species] Error 2
>
>
>>>>>> "Hilmar" == Hilmar Lapp <hlapp at gnf.org> writes:
>
> Hilmar> You need the latest CVS HEAD revision from both biosql-schema
> Hilmar> and bioperl-db. Earlier versions of biosql-schema will not work
> Hilmar> with the latest bioperl-db. It sounds like you're not running
> Hilmar> the latest bioperl-db? Is NP_000358 the first entry in your
> Hilmar> input file? There should have been some DBI-generated noise
> Hilmar> preceding that stack trace.
>
> Hilmar> did bioperl-db pass all tests? Specifically, what's the output
> Hilmar> for
>
> Hilmar> $ make test_species TEST_VERBOSE=1
>
> Hilmar> If any one of those tests fails, please do
>
> Hilmar> $ setenv HARNESS_VERBOSE 1 # csh, tcsh or $ export
> Hilmar> HARNESS_VERBOSE=1 # ksh, bash
>
> Hilmar> then run the above command again and send me the output.
>
> Hilmar> -hilmar
>
> Hilmar> On Tuesday, April 22, 2003, at 10:16 AM, Steve Mathias wrote:
>
>>> Hello All,
>>>
>>> I cannot seem to find a version of the BioSQL schema that will work
>>> with load_sequence_database.pl and bioperl-1.2.1.  I've tried both
>>> the current cvs version of the schema as well as the
>>> before-singapore-change version (the respective stack traces are
>>> pasted below).  Can anyone point me at a BioSQL schema (MySQL or
>>> Postgres) that will work with bioperl-1.2.1?
>>>
>>> Thanks.
>>>
>>> Steve
>>>
>>> Message w/ latest CVS schema:
>>>
>>> ------------- EXCEPTION: Bio::Root::Exception ------------- MSG:
>>> Could not store NP_000358: ------------- EXCEPTION:
>>> Bio::Root::Exception ------------- MSG: error while executing
>>> statement in Bio::DB::BioSQL::SpeciesAdaptor::find_by_unique_key:
>>> Unknown column 'taxon_name.ncbi_taxon_id' in 'field list' STACK:
>>> Error::throw STACK: Bio::Root::Root::throw
>>> /usr/local/lib/perl5/site_perl/5.6.1/Bio/Root/Root.pm:342 STACK:
>>> Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key
>>> /usr/local/lib/perl5/site_perl/5.6.1/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:898 STACK:
>>> Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key
>>> /usr/local/lib/perl5/site_perl/5.6.1/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:809 STACK:
>>> Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>> /usr/local/lib/perl5/site_perl/5.6.1/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:180 STACK:
>>> Bio::DB::Persistent::PersistentObject::create
>>> /usr/local/lib/perl5/site_perl/5.6.1/Bio/DB/Persistent/
>>> PersistentObject.pm:242 STACK:
>>> Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>> /usr/local/lib/perl5/site_perl/5.6.1/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:167 STACK:
>>> Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>> /usr/local/lib/perl5/site_perl/5.6.1/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:238 STACK:
>>> Bio::DB::Persistent::PersistentObject::store
>>> /usr/local/lib/perl5/site_perl/5.6.1/Bio/DB/Persistent/
>>> PersistentObject.pm:266 STACK: ./load_seqdatabase.pl:433
>>> -----------------------------------------------------------
>>>
>>> Message w/ before-singapore-change schema:
>>>
>>> ------------- EXCEPTION: Bio::Root::Exception ------------- MSG:
>>> Could not store NP_000358: ------------- EXCEPTION:
>>> Bio::Root::Exception ------------- MSG: error while executing
>>> statement in Bio::DB::BioSQL::SpeciesAdaptor::find_by_unique_key:
>>> Table 'biosql.taxon_name' doesn't exist STACK: Error::throw STACK:
>>> Bio::Root::Root::throw
>>> /usr/local/lib/perl5/site_perl/5.6.1/Bio/Root/Root.pm:342 STACK:
>>> Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key
>>> /usr/local/lib/perl5/site_perl/5.6.1/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:898 STACK:
>>> Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key
>>> /usr/local/lib/perl5/site_perl/5.6.1/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:809 STACK:
>>> Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>> /usr/local/lib/perl5/site_perl/5.6.1/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:180 STACK:
>>> Bio::DB::Persistent::PersistentObject::create
>>> /usr/local/lib/perl5/site_perl/5.6.1/Bio/DB/Persistent/
>>> PersistentObject.pm:242 STACK:
>>> Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>> /usr/local/lib/perl5/site_perl/5.6.1/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:167 STACK:
>>> Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>> /usr/local/lib/perl5/site_perl/5.6.1/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:238 STACK:
>>> Bio::DB::Persistent::PersistentObject::store
>>> /usr/local/lib/perl5/site_perl/5.6.1/Bio/DB/Persistent/
>>> PersistentObject.pm:266 STACK: ./load_seqdatabase.pl:433
>>> -----------------------------------------------------------
>>>
>>> -- 
>>> -------------------------------------------------------------
>>> Steve Mathias email: smathias at unm.edu UNM Office of Biocomputing
>>> phone: (505) 272-8111
>>> -------------------------------------------------------------
>>> _______________________________________________ Bioperl-l mailing
>>> list Bioperl-l at bioperl.org
>>> http://bioperl.org/mailman/listinfo/bioperl-l
>>>
> Hilmar> --  
> -------------------------------------------------------------
> Hilmar> Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121
> Hilmar> phone: +1-858-812-1757
> Hilmar> -------------------------------------------------------------
>
>
> -- 
> -------------------------------------------------------------
> Steve Mathias                         email: smathias at unm.edu
> UNM Office of Biocomputing              phone: (505) 272-8111
> -------------------------------------------------------------
>
-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------

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