[Bioperl-l] Biosql schema for use w/ bioperl-1.2.1
Steve Mathias
smathias at unm.edu
Tue Apr 22 15:30:39 EDT 2003
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 $)
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
-------------------------------------------------------------
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